Contacts of the helix formed by residues 162 - 174 (chain I) in PDB entry 3SWD
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 162 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 3.8 24.9 - - - -
158I MET* 5.4 2.6 - - - +
160I LYS 3.4 2.6 + - - -
161I VAL* 1.3 77.6 - - - +
163I VAL* 1.3 63.4 + - - +
165I ALA* 3.0 23.9 + - - +
166I THR* 2.9 31.4 + - - -
184I ASN 5.2 0.6 + - - -
186I ALA* 3.9 5.6 - - - +
501I EPZ 2.9 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PRO* 6.5 0.2 - - + -
95I TRP* 4.8 9.9 - - + -
161I VAL* 4.4 1.7 - - + +
162I SER* 1.3 70.9 - - - +
164I GLY* 1.3 62.4 + - - +
166I THR* 3.9 1.7 - - - -
167I VAL* 3.2 25.0 + - + +
186I ALA* 3.8 9.6 - - + +
188I GLU* 3.5 42.6 - - + +
190I GLU* 6.0 4.7 - - + +
191I ILE* 4.0 14.5 - - + +
501I EPZ 2.6 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I TRP* 3.1 24.8 + - - -
125I HIS* 3.1 19.8 - - - -
162I SER* 3.2 3.0 + - - -
163I VAL* 1.3 75.5 - - - +
165I ALA* 1.3 55.6 + - - +
167I VAL 3.3 1.6 + - - -
168I THR 3.0 21.8 + - - -
501I EPZ 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 3.7 21.5 - - + +
125I HIS* 3.3 21.4 + - + -
158I MET* 3.6 24.7 - - + -
162I SER* 3.0 18.9 + - - +
164I GLY* 1.3 72.1 - - - +
166I THR* 1.3 66.9 + - - +
168I THR* 3.1 1.0 + - - -
169I ILE* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I MET* 4.2 14.4 - - - -
162I SER 2.9 23.1 + - - -
165I ALA* 1.3 75.7 - - - +
167I VAL* 1.3 58.2 + - - +
169I ILE* 5.1 0.2 - - - -
170I MET* 3.0 28.2 + - + +
182I ILE* 4.1 8.3 - - + +
185I ALA* 3.8 15.5 - - + +
186I ALA 3.1 15.6 + - - -
191I ILE* 3.7 28.7 - - + -
213I ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PRO* 4.1 23.3 - - + +
95I TRP* 3.7 29.8 - - + +
163I VAL* 3.2 15.7 + - + +
164I GLY 3.7 7.2 - - - +
165I ALA 3.1 0.4 - - - -
166I THR* 1.3 76.2 - - - +
168I THR* 1.3 65.9 + - - +
170I MET* 4.5 11.7 - - + -
171I CYS* 3.0 38.3 + - - -
190I GLU 5.9 0.4 - - - -
191I ILE* 3.9 26.5 - - + -
194I THR* 4.7 4.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
94I ILE 5.0 2.3 + - - +
95I TRP* 3.5 16.2 + - - -
97I LEU* 6.0 1.6 - - + -
98I GLY* 4.5 13.8 + - - +
99I PRO* 6.1 1.1 - - - -
125I HIS* 2.7 44.5 + - + +
129I LEU* 4.1 31.6 - - + -
164I GLY 3.0 7.4 + - - -
165I ALA* 3.1 6.7 + - - +
167I VAL* 1.3 77.9 - - - +
169I ILE* 1.3 63.8 + - + +
171I CYS* 4.1 2.2 - - - +
172I ALA* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU 4.4 3.4 - - - +
125I HIS 5.1 0.2 - - - +
128I GLY* 3.7 32.1 - - - -
129I LEU* 5.2 0.7 - - + -
132I LEU* 4.1 11.1 - - + +
156I ILE* 3.8 28.7 - - + -
158I MET* 3.5 37.2 - - + -
165I ALA* 3.0 12.0 + - - +
166I THR* 5.2 0.4 - - - -
168I THR* 1.3 78.3 - - + +
170I MET* 1.3 66.5 + - - +
172I ALA* 3.3 5.5 + - - +
173I ALA* 3.0 22.7 + - - +
180I THR* 4.6 5.4 - - + -
182I ILE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 170 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I THR* 3.0 21.0 + - + +
167I VAL* 4.1 10.3 - - + +
168I THR 3.4 0.2 - - - -
169I ILE* 1.3 78.1 - - - +
171I CYS* 1.3 61.9 + - - +
173I ALA* 3.5 7.8 + - - +
174I THR* 3.5 15.2 + - - +
182I ILE* 3.8 15.0 - - + +
191I ILE* 3.8 30.3 - - + +
194I THR* 4.2 15.9 - - + -
195I ALA* 3.9 30.3 - - - +
198I LEU* 4.5 4.7 - - + -
205I ILE* 4.2 15.5 - - + -
208I GLN* 5.3 0.2 - - - -
213I ILE* 4.2 25.8 - - - -
215I ILE* 4.2 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 171 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PRO 5.3 1.1 - - - -
31I ALA* 4.1 20.2 - - - -
34I LEU* 3.5 19.4 - - + +
99I PRO* 4.6 15.7 - - + -
167I VAL* 3.0 35.6 + - - +
168I THR* 4.2 2.7 - - - +
170I MET* 1.3 75.9 - - - +
172I ALA* 1.3 61.5 + - - +
173I ALA 3.3 0.2 + - - -
174I THR* 2.8 26.0 + - - -
194I THR* 4.2 6.7 - - - -
198I LEU* 3.8 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I GLY* 4.2 9.8 - - - +
102I ALA* 3.4 27.8 - - + +
129I LEU* 3.8 23.8 - - + -
132I LEU* 3.9 8.7 - - + -
151I LEU* 3.9 20.5 - - + +
168I THR 3.2 17.5 + - - +
169I ILE 3.3 0.4 + - - +
171I CYS* 1.3 76.4 - - - +
173I ALA* 1.3 61.6 + - - +
174I THR 3.4 0.7 + - - -
175I LEU 3.5 5.5 + - - -
176I ALA* 3.9 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I LEU* 4.0 6.2 - - + +
169I ILE 3.0 16.7 + - - +
170I MET 3.8 5.8 - - - +
171I CYS 3.2 0.2 - - - -
172I ALA* 1.3 72.9 - - - +
174I THR* 1.3 62.5 + - - +
175I LEU 2.9 7.6 + - - -
176I ALA* 3.0 21.8 + - - +
178I GLY 5.2 0.3 - - - +
180I THR* 3.5 36.1 + - + +
215I ILE* 3.7 19.8 - - + +
217I GLY* 3.8 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LEU* 3.5 14.7 - - - +
170I MET 3.5 15.5 - - - +
171I CYS 2.8 16.5 + - - +
172I ALA 3.3 0.2 - - - -
173I ALA* 1.3 75.7 - - - +
175I LEU* 1.3 60.1 + - - +
176I ALA 3.6 0.2 - - - -
198I LEU* 3.9 18.2 - - + -
203I ALA* 3.8 30.7 - - + +
205I ILE* 4.1 4.5 - - + -
215I ILE* 3.8 16.2 - - + -
216I GLU 5.1 0.7 - - - -
217I GLY* 3.6 2.4 - - - -
218I VAL* 3.1 32.2 + - - +
221I LEU* 3.7 8.1 - - - +
----------------------------------------------------------
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