Contacts of the helix formed by residues 172 - 187 (chain I) in PDB entry 2QC8
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 GLY 172 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I LEU* 3.8 10.0 - - - +
147I PHE* 3.6 25.0 - - - -
170I ALA 3.7 2.0 + - - -
171I TYR* 1.3 73.9 - - - +
173I ARG* 1.3 67.1 + - - +
174I ASP* 3.1 5.5 + - - -
175I ILE* 3.2 25.2 + - - +
176I VAL* 3.6 4.5 + - - +
202I TRP* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H MET* 4.4 17.1 - - - +
42H CYS* 4.7 7.0 - - - -
227H ARG* 3.6 33.5 - - - +
230H GLU* 2.7 47.2 + - - +
164I GLY 3.1 25.9 + - - -
165I VAL* 3.6 10.1 - - - +
170I ALA* 3.3 11.9 + - + +
171I TYR 3.7 1.4 - - - -
172I GLY* 1.3 76.4 - - - +
174I ASP* 1.3 55.1 + - - +
176I VAL* 2.8 8.8 + - + +
177I GLU* 2.7 57.5 + - + +
202I TRP* 3.9 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ASN 4.5 7.8 + - - +
11H LYS* 2.6 47.2 + - - +
14H LYS* 3.5 31.5 + - + +
231H ASP* 4.4 2.8 - - - +
172I GLY* 3.1 1.9 + - - -
173I ARG* 1.3 77.0 - - - +
175I ILE* 1.3 54.8 + - + +
177I GLU* 3.5 3.0 + - - +
178I ALA* 2.8 37.4 + - - +
232I PHE* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I TYR* 4.4 3.1 - - - +
139I LEU* 3.9 28.5 - - + -
147I PHE* 5.2 7.2 - - + -
172I GLY* 3.5 19.1 - - - +
174I ASP* 1.3 76.5 - - + +
176I VAL* 1.3 70.0 + - - +
178I ALA* 3.2 1.0 + - - +
179I HIS* 2.8 25.1 + - - +
225I LEU* 4.1 14.6 - - + -
228I VAL* 3.9 5.9 - - + +
229I CYS* 4.0 14.6 - - - -
232I PHE* 3.8 42.4 - - + -
234I VAL* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ARG* 6.0 0.9 - - - +
137I TYR* 3.5 20.6 - - - +
139I LEU* 5.3 0.2 - - + -
172I GLY 3.9 8.1 - - - +
173I ARG* 2.8 15.9 + - + +
175I ILE* 1.3 75.9 - - + +
177I GLU* 1.3 68.1 + - - +
179I HIS* 3.7 5.1 + - - +
180I TYR* 3.0 23.1 + - + +
193I THR* 3.9 34.6 - - + +
202I TRP* 3.3 49.8 - - + -
203I GLU 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LYS* 3.9 27.5 + - - +
18H MET* 4.4 12.3 - - - +
27H GLN* 4.8 2.9 + - - -
29H MET* 4.4 4.0 - - - +
89H PHE 5.5 0.2 - - - +
90H ARG* 2.8 53.5 + - - +
227H ARG* 4.6 7.8 + - - +
173I ARG* 2.7 49.9 + - + +
174I ASP 3.7 4.0 - - - +
176I VAL* 1.3 76.3 - - - +
178I ALA* 1.3 61.3 + - - +
180I TYR* 3.3 6.1 + - - +
181I ARG* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LYS* 4.9 5.6 - - + +
17H TYR* 3.6 43.7 - - + -
18H MET* 5.3 1.1 - - - -
174I ASP 2.8 22.3 + - - +
175I ILE 3.2 3.1 + - - +
177I GLU* 1.3 72.5 - - - +
179I HIS* 1.3 52.4 - - - +
181I ARG* 3.2 5.6 + - - +
182I ALA* 2.8 34.5 + - - +
228I VAL* 3.9 12.6 - - + -
232I PHE* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 179 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I TYR* 5.6 0.8 + - - -
175I ILE 2.8 21.4 + - - +
176I VAL* 3.7 5.3 + - - +
178I ALA* 1.3 71.0 - - - +
180I TYR* 1.3 66.7 + - - +
182I ALA* 3.5 1.3 - - - +
183I CYS* 2.9 50.9 + - - -
190I ILE* 4.3 5.1 - - + +
193I THR* 5.8 1.4 - - - +
204I PHE* 3.4 45.6 - + - +
221I ALA 2.9 22.0 + - - -
224I ILE* 3.5 12.8 - - + -
225I LEU* 3.3 39.8 + - + +
228I VAL* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLN* 3.3 28.9 - - + +
44H THR* 3.6 17.3 - - + -
45H ARG 3.3 7.6 + - - -
46H THR* 2.7 43.7 + - - -
90H ARG* 4.5 4.9 - - - -
176I VAL* 3.0 17.6 + - + +
177I GLU* 3.3 8.0 + - - +
179I HIS* 1.3 76.3 + - - +
181I ARG* 1.3 62.1 + - - +
183I CYS* 3.8 2.1 - - - +
184I LEU* 3.2 32.1 + - + +
190I ILE* 3.7 29.6 - - + -
192I GLY* 3.3 9.7 - - - -
193I THR* 3.3 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H TYR 3.4 25.8 - - - +
18H MET* 3.0 54.3 + - - +
20H LEU* 3.2 21.7 + - + +
22H GLN* 3.6 37.6 + - - +
27H GLN* 3.8 16.8 + - - +
90H ARG 3.1 26.7 + - - -
94H ASN* 3.9 4.0 - - - +
177I GLU 3.1 13.6 + - - +
178I ALA* 3.6 4.5 - - - +
180I TYR* 1.3 81.8 - - - +
182I ALA* 1.3 60.9 + - - +
184I LEU* 3.5 8.0 + - - +
185I TYR* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H TYR* 4.3 15.5 - - + -
20H LEU* 4.4 5.3 - - - +
88I PRO* 3.6 26.2 - - + +
89I PHE* 5.1 0.2 - - + -
178I ALA 2.8 17.0 + - - +
179I HIS* 3.5 6.7 - - - +
181I ARG* 1.3 76.8 - - - +
183I CYS* 1.3 52.0 + - - +
185I TYR* 3.4 1.0 + - - +
186I ALA* 2.8 35.7 + - - +
224I ILE* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 183 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I HIS* 2.9 52.7 + - - +
180I TYR 3.8 4.5 - - - +
182I ALA* 1.3 74.9 - - - +
184I LEU* 1.3 60.0 + - - +
186I ALA* 3.2 3.8 + - - -
187I GLY 2.9 8.5 + - - -
188I VAL* 2.8 54.6 + - + +
190I ILE* 3.9 18.2 - - + -
221I ALA* 4.5 4.3 - - - -
224I ILE* 4.1 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 4.0 38.0 - - + +
25H LYS* 3.9 32.5 - - + -
27H GLN* 4.3 18.8 - - + +
46H THR* 4.3 9.4 - - + -
86I ARG* 5.2 0.7 + - - -
180I TYR* 3.2 35.6 + - + +
181I ARG* 3.8 7.9 - - - +
182I ALA 3.4 0.2 - - - -
183I CYS* 1.3 76.7 - - - +
185I TYR* 1.3 62.0 + - - +
187I GLY* 3.1 14.2 + - - -
188I VAL 4.4 5.8 - - - +
190I ILE* 3.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 3.8 25.4 - - + -
21H PRO* 3.3 49.1 + - + +
22H GLN* 4.7 2.2 + - - +
86I ARG* 2.9 63.4 + - + +
87I ASP 3.7 19.7 - - - -
88I PRO* 3.7 20.0 - - + -
91I LYS* 3.6 14.0 - - - +
92I ASP* 3.1 31.6 + - - +
181I ARG 3.1 15.4 + - - +
182I ALA 3.6 3.6 - - - +
184I LEU* 1.3 80.6 - - - +
186I ALA* 1.3 61.1 + - - +
187I GLY* 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I PHE* 3.4 13.3 - - + +
86I ARG* 3.0 48.6 + - - +
88I PRO* 4.4 2.7 - - + -
96I LEU* 5.0 0.2 - - + -
182I ALA 2.8 18.4 + - - +
183I CYS* 3.2 5.4 + - - +
185I TYR* 1.3 78.2 - - - +
187I GLY* 1.3 58.6 + - - +
188I VAL* 3.5 5.8 - - + +
224I ILE* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I PHE* 3.7 9.3 - - - -
86I ARG* 5.9 1.1 - - - -
183I CYS 2.9 4.0 + - - -
184I LEU 3.1 11.3 + - - -
185I TYR 3.2 0.6 - - - -
186I ALA* 1.3 78.4 - - - +
188I VAL* 1.3 65.3 + - - +
189I LYS* 3.7 0.7 + - - +
217I HIS* 3.4 14.9 - - - -
----------------------------------------------------------
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