Contacts of the strand formed by residues 9 - 16 (chain B) in PDB entry 5GOW
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 LEU 9 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 4.3 15.3 - - + +
8B VAL* 1.3 80.5 - - - +
10B LEU* 1.3 61.4 + - - +
11B ILE* 4.3 1.1 - - - -
26B LEU 2.7 8.1 + - - +
27B MET 4.3 1.8 - - - -
28B ALA* 3.8 37.0 - - + +
95B LEU* 4.1 16.8 - - + +
99B LEU* 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.3 4.3 - - - +
9B LEU* 1.3 82.1 - - - +
11B ILE* 1.3 64.3 + - - +
12B VAL* 3.6 11.0 - - + -
24B LEU 3.8 0.5 - - - +
25B TYR* 3.2 5.2 - - - -
26B LEU* 2.8 62.8 + - + +
88B GLU* 6.2 1.3 - - + -
91B ALA* 3.7 27.8 - - + +
92B VAL* 3.4 30.5 - - + +
95B LEU* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.6 24.5 - - + +
9B LEU 5.6 0.7 - - - -
10B LEU* 1.3 77.7 - - - +
12B VAL* 1.3 70.8 + - - +
13B LYS* 4.4 18.2 - - + -
23B ALA* 5.6 0.4 - - + -
24B LEU 3.6 1.6 - - - -
25B TYR* 3.4 28.0 - - + -
88B GLU* 4.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.6 24.5 - - + +
11B ILE* 1.3 81.4 - - - +
13B LYS* 1.3 64.0 + - - +
15B VAL* 3.5 12.3 - - + -
23B ALA* 3.4 9.0 - - - +
24B LEU* 2.6 65.0 + - + +
79B PHE* 3.2 29.6 - - + -
88B GLU* 3.0 26.9 - - + +
92B VAL* 3.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.4 17.0 - - + -
12B VAL* 1.3 78.9 - - - +
14B LYS* 1.3 74.3 + - + +
15B VAL* 3.0 14.9 - - - +
22B GLY 3.7 2.0 - - - -
23B ALA* 4.4 7.6 - - + +
79B PHE* 5.0 0.2 - - - -
81B ASN* 2.8 33.3 + - - +
84B THR* 3.1 13.7 + - - -
88B GLU* 2.6 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 1.3 76.9 - - + +
15B VAL* 1.3 51.8 + - - +
21B ASP* 2.6 41.5 + - - +
22B GLY 3.2 6.3 + - - -
23B ALA* 4.7 0.4 - - - +
36B GLU* 2.6 43.1 + - - +
79B PHE 3.8 0.2 - - - -
80B SER* 2.8 39.5 + - - +
81B ASN* 3.0 31.1 + - + +
82B GLU* 5.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.5 22.9 - - + -
13B LYS 3.0 20.6 + - - +
14B LYS* 1.3 73.4 - - - +
16B ARG* 1.3 61.7 + - - +
21B ASP* 3.5 0.4 + - - -
22B GLY 2.7 32.8 + - - +
24B LEU* 4.3 8.3 - - + +
33B TRP* 2.8 36.4 + - + +
77B PHE* 3.6 35.2 - - + -
78B HIS 3.3 7.0 - - - +
79B PHE* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 2.7 32.8 + - - +
398A GLU* 2.7 31.3 + - - -
15B VAL* 1.3 72.1 - - - +
17B GLN* 1.3 59.8 + - - +
18B LYS 4.0 0.7 - - - -
19B LYS* 4.0 20.3 - - - +
20B GLN 3.0 6.3 - - - +
21B ASP* 3.2 38.1 - - - +
77B PHE* 3.6 2.3 - - - -
78B HIS* 2.6 74.4 + - + +
80B SER* 3.6 8.5 - - - +
----------------------------------------------------------
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