Contacts of the helix formed by residues 153 - 174 (chain I) in PDB entry 6GYS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 153 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I ARG* 5.8 0.5 - - - -
151I ASN 2.9 11.0 + - - -
152I HIS* 1.3 71.0 - - - +
154I VAL* 1.3 54.5 + - - +
155I ASP* 4.7 0.3 + - - +
156I GLY* 3.0 20.3 + - - -
157I LYS* 2.6 35.9 + - - +
85J LEU 3.7 0.4 - - - -
86J THR* 3.3 38.2 - - - -
87J ARG* 4.7 1.3 - - - -
88J THR 3.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I SER* 1.3 69.7 - - - +
155I ASP* 1.3 58.7 + - - +
157I LYS* 3.1 11.9 + - - +
158I TYR* 3.0 45.7 + - + -
222I GLN 5.2 0.2 - - - +
223I CYS* 3.3 29.7 - - - +
224I ASP* 5.8 1.6 - - - +
228I HIS* 4.0 11.9 - - + +
85J LEU* 2.9 28.4 + - + +
88J THR* 3.1 33.9 + - + +
89J PRO 3.8 12.8 - - - +
90J ALA* 4.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I SER* 5.1 0.2 + - - -
154I VAL* 1.3 76.8 - - - +
156I GLY* 1.3 57.0 + - - +
158I TYR* 3.0 6.7 + - - -
159I TRP* 2.8 46.6 + - - -
230I ASP* 4.7 1.4 - - - +
232I ARG* 2.4 41.4 + - - +
85J LEU* 2.9 32.0 + - + +
86J THR* 3.8 23.1 - - + +
560J LYS* 4.1 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I ARG* 3.5 13.4 + - - -
153I SER* 3.0 24.2 + - - -
155I ASP* 1.3 78.9 + - - +
157I LYS* 1.3 55.9 + - - +
159I TRP* 3.2 14.0 + - - +
160I ASP* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I HIS* 3.7 34.9 + - + -
153I SER 2.6 22.0 + - - +
154I VAL* 3.1 10.7 + - - +
156I GLY* 1.3 70.6 - - - +
158I TYR* 1.3 59.1 + - - +
160I ASP* 3.2 11.1 + - - +
161I ALA* 2.9 29.3 + - - +
219I GLN* 3.1 47.5 - - - +
222I GLN* 2.9 32.7 + - - -
223I CYS* 3.5 15.6 - - - -
90J ALA* 3.8 18.8 - - + -
92J LEU* 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 158 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I VAL* 3.0 46.6 + - + -
155I ASP* 3.0 2.2 + - - +
157I LYS* 1.3 74.8 - - - +
159I TRP* 1.3 59.0 + - - +
161I ALA* 3.4 3.3 + - - +
162I LEU* 2.8 30.3 + - - +
220I LEU* 3.6 18.2 - - + +
223I CYS* 3.5 23.2 + - + -
225I PHE* 3.3 20.4 - - + -
228I HIS* 2.3 37.3 + - + +
230I ASP* 4.9 12.8 - - + -
232I ARG* 3.2 39.5 - - + +
233I LEU* 4.5 21.3 - - + -
85J LEU* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 159 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I GLU* 3.9 21.8 - - + -
139I ARG* 3.5 38.8 - - + +
146I ARG* 3.7 23.3 + - - +
155I ASP* 2.8 45.5 + - - -
156I GLY* 3.2 10.5 + - - +
158I TYR* 1.3 75.0 - - - +
160I ASP* 1.3 62.9 + - - +
162I LEU* 3.4 46.8 - - + +
163I ILE* 3.5 10.2 + - - +
232I ARG* 2.9 38.5 - - - +
560J LYS 4.5 1.8 - - - -
561J GLY 4.4 3.6 - - - -
562J LEU 4.5 2.2 - - - -
563J GLY* 3.5 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I TYR* 3.1 21.9 - - + -
146I ARG* 2.4 49.5 + - - +
152I HIS* 4.8 4.3 - - - -
156I GLY 2.8 24.2 + - - +
157I LYS* 3.4 20.8 + - - +
159I TRP* 1.3 76.6 - - - +
161I ALA* 1.3 60.1 + - - +
163I ILE* 3.3 17.2 - - - +
164I TRP* 3.1 15.4 + - - -
219I GLN* 3.1 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I LYS 2.9 14.8 + - - +
158I TYR 4.0 1.1 - - - +
160I ASP* 1.3 73.2 - - - +
162I LEU* 1.3 66.1 + - - +
164I TRP* 3.2 6.9 + - - -
165I SER* 3.0 13.9 + - - -
216I SER* 2.9 47.3 + - - +
219I GLN* 2.9 13.9 + - + +
220I LEU* 3.7 20.0 - - + -
236I ALA* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I ILE* 5.1 22.7 - - + -
136I LEU* 4.0 23.3 - - + -
139I ARG* 5.5 0.2 - - + -
158I TYR 2.8 20.0 + - - +
159I TRP* 3.4 41.5 - - + +
160I ASP 3.2 0.2 - - - -
161I ALA* 1.3 75.4 - - - +
163I ILE* 1.3 59.0 + - + +
165I SER* 2.3 32.3 + - - +
166I VAL* 2.9 18.4 + - + +
232I ARG* 4.8 14.8 - - + +
235I GLN* 5.1 4.3 - - - +
236I ALA* 4.3 20.4 - - + +
239I ILE* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I LEU* 3.8 23.1 - - + -
139I ARG* 4.3 11.9 - - + +
140I VAL* 4.0 18.4 - - + +
143I TYR* 3.5 46.0 - - + -
159I TRP 3.7 11.2 - - - +
160I ASP 3.3 16.1 + - - +
162I LEU* 1.3 74.6 - - + +
164I TRP* 1.3 61.8 + - + +
166I VAL* 3.5 8.5 - - + +
167I PHE* 2.8 61.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I CYS* 5.2 0.4 - - - -
102I TRP* 3.3 37.9 - - + -
103I MET* 3.5 16.8 - - + -
106I LEU* 4.5 6.1 - - + -
143I TYR* 3.3 24.4 + + - -
147I ARG* 3.8 4.0 - - - -
160I ASP 3.1 15.1 + - - -
161I ALA* 3.2 8.3 + - - +
163I ILE* 1.3 79.9 - - + +
165I SER* 1.3 51.2 + - - +
167I PHE* 3.3 12.2 + + - +
168I THR* 2.7 37.6 + - - -
212I PHE* 3.3 54.5 - + - +
215I CYS* 3.4 29.4 + - + -
216I SER 3.5 5.4 - - - +
219I GLN* 3.0 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I ALA 3.0 9.1 + - - -
162I LEU* 2.3 32.6 + - - +
164I TRP* 1.3 76.3 - - - +
166I VAL* 1.3 62.0 + - - +
168I THR* 3.2 10.8 - - - -
169I MET 3.0 17.7 + - - -
216I SER* 4.0 6.1 - - - -
236I ALA* 3.5 38.7 - - - +
239I ILE* 3.3 15.6 - - - +
240I LEU* 4.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I MET* 3.6 30.7 - - + -
126I TYR* 6.3 2.0 - - + -
130I ILE* 5.4 3.6 - - + -
136I LEU* 3.7 36.6 - - + -
162I LEU* 2.9 25.3 + - + +
163I ILE* 3.5 10.3 - - - +
164I TRP 3.2 0.2 - - - -
165I SER* 1.3 76.8 - - - +
167I PHE* 1.3 58.3 + - - +
169I MET* 3.2 13.6 + - + +
170I CYS* 2.9 36.9 + - - -
239I ILE* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I LEU* 3.7 29.6 - - + -
111I SER* 3.6 31.0 - - - -
114I LEU* 4.3 14.4 - - + -
115I MET* 3.8 27.1 - - + -
140I VAL* 4.5 4.9 - - + -
163I ILE* 2.8 53.7 + - + +
164I TRP* 3.6 21.8 - + - +
165I SER 3.3 0.2 - - - -
166I VAL* 1.3 73.9 - - - +
168I THR* 1.3 59.7 + - - +
170I CYS* 3.2 6.2 + - - +
171I ILE* 2.9 35.0 + - - +
212I PHE* 3.6 22.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I TRP 2.7 20.9 + - - -
165I SER* 3.2 10.5 - - - -
167I PHE* 1.3 75.6 - - - +
169I MET* 1.3 57.2 + - - +
171I ILE* 3.2 3.0 + - - +
172I TYR* 3.0 21.8 + - - +
209I CYS* 3.3 41.6 - - - +
212I PHE* 3.1 8.5 + - - +
213I ALA* 3.0 25.5 + - + -
239I ILE 5.5 0.4 - - - +
240I LEU* 3.7 20.4 - - + -
243I THR* 3.8 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I ALA* 5.7 1.8 - - + -
122I LEU* 3.9 24.4 - - + +
125I LEU* 4.0 22.2 - - + -
126I TYR* 4.1 35.7 - - + +
165I SER 3.0 5.7 + - - -
166I VAL* 3.2 17.2 + - + +
168I THR* 1.3 77.6 - - - +
170I CYS* 1.3 61.5 + - - +
172I TYR* 3.0 24.0 + - + +
173I TYR* 3.4 14.4 + - + -
239I ILE* 3.7 41.0 + - + -
242I THR* 4.1 16.2 - - - +
243I THR* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 170 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LEU* 3.7 40.7 - - + +
115I MET* 4.4 6.5 - - - -
117I PHE* 5.6 1.0 - - - -
118I ALA* 3.7 30.3 - - + -
122I LEU* 4.8 2.4 - - - +
166I VAL* 2.9 37.6 + - - +
167I PHE* 3.2 6.9 + - - +
169I MET* 1.3 77.0 - - - +
171I ILE* 1.3 62.4 + - - +
173I TYR 4.1 0.5 - - - -
174I MET* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LEU* 3.8 15.5 - - + -
167I PHE 2.9 19.0 + - - +
168I THR 3.6 7.2 - - - +
170I CYS* 1.3 75.3 - - - +
172I TYR* 1.3 62.3 + - - +
173I TYR 3.1 1.4 + - - -
174I MET* 3.5 5.2 + - - +
179I LEU* 3.7 25.1 - - + -
183I PHE* 4.2 2.5 - - + -
205I GLN* 3.3 58.2 + - + +
206I LEU* 5.4 0.2 - - - -
208I MET* 3.7 16.8 - - + -
209I CYS* 3.7 13.0 - - + +
212I PHE* 3.5 26.7 - - + -
499I ILE* 3.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I THR 3.0 12.4 + - - +
169I MET* 3.0 16.8 + - - +
171I ILE* 1.3 77.6 - - - +
173I TYR* 1.3 85.7 + + + +
206I LEU* 4.4 3.1 - - + -
209I CYS* 4.2 10.3 - - - -
242I THR* 3.2 25.8 - - - -
243I THR* 3.6 16.4 - - + -
244I THR* 3.3 39.5 - - + +
455I ARG* 2.7 46.4 + - - -
457I PRO* 3.2 16.7 - - + +
499I ILE* 3.3 27.6 - - + +
500I PHE* 3.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I PHE* 4.0 4.7 - - + -
122I LEU* 3.6 38.1 - - + -
125I LEU* 3.8 18.5 - - + +
169I MET* 3.4 12.2 + - + -
170I CYS 4.1 0.4 - - - -
171I ILE 3.2 0.2 - - - -
172I TYR* 1.3 98.4 - + - +
174I MET* 1.3 62.1 + - - +
175I PRO* 3.3 2.9 - - - +
242I THR* 5.3 3.1 - - - -
398I PHE* 4.2 13.5 - + - -
452I PHE* 3.2 59.9 - + + +
455I ARG* 3.0 31.4 - - + +
456I HIS* 3.1 44.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LEU* 3.7 33.0 - - + -
117I PHE* 3.6 41.3 - - + -
170I CYS* 3.1 20.5 + - + +
171I ILE 3.5 3.0 + - - +
173I TYR* 1.3 76.4 - - - +
175I PRO* 1.3 76.9 - - + +
178I LYS* 3.8 12.1 - - + -
179I LEU* 3.8 29.6 - - + +
182I ILE* 3.7 21.1 - - + -
205I GLN* 2.9 19.6 + - - -
455I ARG* 2.5 20.4 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il