Contacts of the strand formed by residues 3 - 7 (chain R) in PDB entry 1G3I
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 ILE 3 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R THR* 3.7 7.2 - - + -
2R THR* 1.3 76.3 - - - +
4R VAL* 1.3 60.2 + - - +
14R VAL* 4.3 11.7 - - + -
15R GLY 3.3 11.4 - - - +
16R GLY* 3.5 21.1 - - - -
33R LYS* 3.7 19.7 - - + +
34R VAL* 4.7 0.2 - - + -
45R GLY* 4.0 23.6 - - - +
46R PHE 3.4 26.7 - - - +
47R ALA* 3.8 14.8 - - + -
96R ILE* 3.9 8.2 - - + +
121R LEU 3.8 0.2 - - - +
122R ALA* 2.9 5.4 - - - +
123R ILE* 2.8 47.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 4 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR 4.1 0.2 + - - -
3R ILE* 1.3 77.5 - - - +
5R SER* 1.3 67.4 + - - +
6R VAL* 4.6 3.4 - - + -
14R VAL* 3.7 0.3 - - - +
15R GLY 2.9 31.5 + - - +
96R ILE* 5.1 0.2 - - - -
120R ILE* 4.3 15.3 - - + -
121R LEU 2.9 11.4 - - - +
122R ALA* 4.0 9.4 - - + -
130R ALA* 3.9 28.7 - - + +
134R ALA* 4.5 4.7 - - + -
149R VAL* 3.6 15.6 - - + +
152R SER* 4.4 6.1 - - - -
153R LEU* 3.3 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 5 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 1.3 73.9 - - - +
6R VAL* 1.3 64.3 + - - +
7R ARG* 5.8 0.5 - - - +
12R VAL* 4.6 5.5 - - - +
13R VAL 2.5 23.6 + - - -
14R VAL* 3.1 22.4 - - - +
96R ILE* 4.1 13.9 - - - -
98R ALA* 4.9 3.8 - - - +
103R SER* 5.2 4.9 - - - -
119R GLN 3.8 1.9 - - - +
120R ILE* 3.2 5.0 - - - +
121R LEU* 2.4 49.3 + - - +
149R VAL* 4.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 4.6 2.5 - - + -
5R SER* 1.3 80.7 + - - +
7R ARG* 1.3 72.5 + - - +
8R ARG* 4.7 2.5 - - + +
13R VAL* 3.1 24.9 + - - +
118R ASP 5.6 0.2 - - - +
119R GLN 4.1 2.5 - - - -
120R ILE* 4.0 21.5 - - + +
134R ALA* 4.1 5.2 - - + -
138R VAL* 3.4 27.4 - - + -
145R ALA* 3.6 23.5 - - - +
148R ILE* 3.6 21.1 - - + -
149R VAL* 3.2 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R SER* 5.8 0.4 - - - +
6R VAL* 1.3 77.1 - - - +
8R ARG* 1.3 71.5 + - - +
10R GLY* 5.8 4.4 - - - +
11R GLN 3.2 12.6 - - - +
12R VAL* 2.7 39.3 - - + +
98R ALA* 4.1 0.8 - - - +
99R ASP 3.3 5.7 + - - -
100R GLU 3.8 8.7 + - - -
101R LYS 3.7 17.1 + - - -
102R GLU* 2.5 38.7 + - - +
103R SER* 3.3 22.8 + - - +
118R ASP 4.0 12.3 - - - +
119R GLN* 3.5 29.6 + - + +
----------------------------------------------------------
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