Contacts of the strand formed by residues 161 - 171 (chain G) in PDB entry 3HEI
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 CYS 161 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL 3.3 2.5 - - - -
43G CYS* 2.1 46.2 - - - -
45G VAL* 3.9 4.1 - - + +
75G VAL* 3.4 3.7 - - - +
76G ARG* 2.9 41.2 + - + +
81G PHE* 3.8 20.4 - - + -
88G CYS* 5.2 0.6 - - - -
89G LYS 4.4 3.0 + - - -
160G ALA* 1.3 73.6 - - - +
162G VAL* 1.3 58.4 - - - +
112H THR 4.0 1.8 - - - -
113H PRO* 3.5 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TRP* 4.1 19.6 - - + -
40G TYR 3.9 0.7 - - - +
41G SER* 3.2 2.8 - - - -
42G VAL* 2.8 39.4 + - + +
73G PHE* 4.6 2.5 - - + -
74G THR 3.4 11.4 - - - +
75G VAL* 3.9 18.6 - - + -
91G THR 5.1 0.7 - - - +
92G PHE* 4.0 33.7 - - + -
157G ASP* 5.4 0.2 - - - +
160G ALA* 3.7 24.2 - - + -
161G CYS* 1.3 78.8 - - - +
163G ALA* 1.3 70.6 + - - +
164G LEU* 4.5 1.6 - - + +
113H PRO* 3.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G MET* 3.8 28.0 - - - -
40G TYR 3.4 4.3 - - - +
41G SER* 4.2 4.5 - - - -
73G PHE* 3.1 7.6 - - - +
74G THR* 2.9 44.5 + - - +
162G VAL* 1.3 76.7 - - - +
164G LEU* 1.3 61.2 + - - +
165G LEU* 3.8 5.6 - - + +
113H PRO* 3.7 14.2 - - + +
114H PHE* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G PHE* 4.2 4.4 - - + -
16G TRP* 4.7 1.8 - - + -
25G TRP* 4.5 11.0 - - + -
39G MET* 3.4 2.8 - - - -
40G TYR* 2.7 39.7 + - + +
54G LEU* 3.9 26.0 - - + -
71G LEU* 4.3 14.4 - - + -
72G LYS 3.7 14.1 - - - +
73G PHE* 4.1 10.1 - - + -
92G PHE* 4.8 9.2 - - + -
155G PHE* 3.9 21.3 - - + -
162G VAL* 4.2 2.0 - - + +
163G ALA* 1.3 71.5 - - - +
165G LEU* 1.3 59.3 + - - +
166G SER 3.7 13.0 - - - +
167G VAL* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C CYS* 4.7 16.8 - - - -
7G PHE* 3.4 19.3 - - - -
8G ALA* 3.8 9.9 - - - +
32G MET* 4.7 7.6 - - - -
37G ILE* 3.7 30.3 - - + -
38G TYR 4.3 4.6 - - - +
39G MET* 4.0 18.4 - - + -
72G LYS* 2.8 10.5 + - + +
73G PHE* 4.8 0.2 - - - -
74G THR* 4.8 2.5 - - + +
136G LEU* 4.1 25.8 - - + -
163G ALA* 3.8 30.3 - - + +
164G LEU* 1.3 76.6 - - - +
166G SER* 1.3 63.9 + - - +
114H PHE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C CYS* 4.9 4.7 - - - -
6G ASP* 4.6 4.5 + - - -
7G PHE* 4.2 4.9 - - - -
8G ALA* 4.2 16.1 - - - +
70G GLU* 4.1 3.3 + - - -
71G LEU* 3.3 5.5 - - - -
72G LYS* 3.0 56.7 + - - +
164G LEU* 3.6 5.2 - - - +
165G LEU* 1.3 82.1 - - - +
167G VAL* 1.3 73.2 + - - +
168G ARG* 4.5 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LEU* 3.6 16.1 - - + +
6G ASP* 3.4 4.0 + - - +
7G PHE* 3.0 32.0 + - + +
16G TRP* 3.8 23.1 - - + -
56G THR* 5.0 0.2 - - + -
69G ILE* 4.7 0.9 - - + -
70G GLU 3.3 4.5 - - - -
71G LEU* 3.9 14.8 - - + -
153G LEU* 4.2 18.6 - - + -
155G PHE* 3.8 17.3 - - + -
164G LEU* 3.7 28.9 - - + -
166G SER* 1.3 80.8 + - - +
168G ARG* 1.3 61.2 + - - +
169G VAL* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLU* 3.5 37.0 + - - +
168C ARG* 3.0 16.8 - - - +
1G GLU* 2.7 37.6 + - - +
3G VAL* 3.5 35.1 - - + +
5G LEU 3.3 8.5 - - - +
6G ASP* 4.2 16.9 + - - +
68G PHE 3.6 1.6 - - - +
69G ILE* 3.5 2.3 - - - -
70G GLU* 2.8 61.8 + - + +
166G SER* 4.8 4.7 - - - +
167G VAL* 1.3 74.1 - - - +
169G VAL* 1.3 61.8 + - - +
170G TYR* 3.1 34.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G VAL* 3.5 2.9 - - - +
4G LEU* 2.7 36.3 + - + -
5G LEU* 2.9 36.4 + - + +
67G ILE* 4.1 19.5 - - + -
68G PHE 3.2 8.3 - - - +
69G ILE* 4.5 5.6 - - + -
151G PHE* 3.8 26.9 - - + -
153G LEU* 3.3 31.4 - - + -
167G VAL* 4.3 4.3 - - + -
168G ARG* 1.3 77.2 - - - +
170G TYR* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G GLU* 3.5 35.6 + - + -
2G VAL 3.1 21.1 - - - +
3G VAL* 3.9 3.8 - - - -
4G LEU* 4.2 5.6 - - - +
67G ILE* 3.6 3.4 - - - -
68G PHE* 2.8 57.7 + - + +
70G GLU* 4.9 4.7 - - + -
140G GLU* 2.6 35.0 + - - -
168G ARG* 3.1 42.6 - - + +
169G VAL* 1.3 79.7 - - - +
171G TYR* 1.3 68.9 + - - +
172G LYS* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G GLU* 3.3 4.5 - - - -
2G VAL* 2.9 77.1 + - + +
4G LEU* 4.0 15.0 - - + -
61G ARG 4.9 0.9 - - - -
62G GLY* 6.2 0.2 - - - -
63G GLU* 4.4 23.2 + - + +
64G ALA* 3.4 43.5 - - + -
65G GLU 5.1 0.9 - - - +
66G ARG 3.5 21.8 - - - +
67G ILE* 4.7 0.4 - - - -
68G PHE* 4.6 1.6 - - - -
170G TYR* 1.3 76.2 - - - +
172G LYS* 1.3 76.6 + - - +
173G LYS* 5.2 4.7 - - + -
----------------------------------------------------------
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