Contacts of the strand formed by residues 38 - 48 (chain B) in PDB entry 1GJ7
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 VAL 38 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.6 33.8 - - + -
35B ARG 3.3 7.4 - - - +
36B ARG* 4.5 10.8 - - + +
37B SER* 1.3 90.3 - - + +
39B THR* 1.3 68.6 + - - +
65B ILE* 4.5 22.9 - - + -
67B TYR* 6.0 2.2 - - + -
74B ASN* 4.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.1 7.4 - - - -
35B ARG* 2.8 35.4 + - - +
37B HIS* 2.6 45.5 + - + +
38B VAL* 1.3 80.4 - - - +
40B TYR* 1.3 68.4 + - - +
41B VAL* 3.9 1.2 - - - +
74B ASN* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.4 17.3 - - - -
32B ALA* 3.7 21.2 - - + -
33B ILE 3.4 9.6 - - - -
34B TYR* 3.7 17.0 - + + -
39B THR* 1.3 81.2 + - - +
41B VAL* 1.3 64.1 - - - +
42B CYS* 3.1 33.8 + - - -
43B GLY* 3.3 10.6 - - - -
73B LEU* 3.5 32.3 - - + -
74B ASN* 5.9 0.8 + - - -
141B PHE* 3.8 16.2 + + + +
151B TYR* 3.8 39.3 - + + -
193B GLY 3.4 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 2.8 16.8 + - + +
34B TYR 3.8 2.5 - - - -
35B ARG* 3.5 42.2 - - + +
39B THR* 3.9 2.2 - - - +
40B TYR* 1.3 85.0 - - - +
42B CYS* 1.3 76.9 + - + +
58B CYS* 3.6 27.8 - - + +
59B PHE* 4.8 4.0 - - + -
64B TYR* 4.1 16.4 - - + -
151B TYR* 4.8 3.5 + - - -
193B GLY* 4.7 7.4 - - - -
251B 132 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 2.9 33.9 + - + +
40B TYR* 3.1 16.3 + - - -
41B VAL* 1.3 90.7 - - + +
43B GLY* 1.3 67.4 + - - +
54B SER* 4.3 1.8 - - - +
58B CYS* 2.0 53.4 - - + -
193B GLY 4.4 2.5 - - - -
195B SER* 3.1 16.6 - - - +
251B 132 3.6 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.9 11.4 - - - -
31B ALA 3.3 8.3 - - - -
33B ILE* 3.8 2.9 - - - +
40B TYR* 3.3 13.9 + - - -
42B CYS* 1.3 78.8 - - - +
44B GLY* 1.3 58.3 + - - -
54B SER* 2.9 21.7 + - - -
193B GLY 4.3 3.0 + - - -
194B ASP* 4.9 1.6 - - - -
195B SER 3.0 9.5 + - - -
196B GLY* 3.2 12.3 - - - -
197B GLY* 4.1 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.7 11.0 - - - -
31B ALA* 2.8 29.6 + - - -
33B ILE* 4.5 1.1 - - - -
43B GLY* 1.3 73.9 - - - -
45B SER* 1.3 66.3 + - - -
52B VAL* 4.1 9.0 - - - -
53B ILE 3.2 14.4 - - - -
54B SER* 4.2 2.5 - - - -
196B GLY 3.5 6.3 + - - -
197B GLY* 4.0 2.9 - - - -
198B PRO* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.2 9.0 - - - -
31B ALA* 4.6 0.9 - - - +
44B GLY* 1.3 76.8 + - - -
46B LEU* 1.3 62.2 + - - +
47B MET* 3.6 0.8 + - - -
52B VAL* 3.1 9.9 - - - +
53B ILE* 2.9 44.9 + - - +
121B ILE* 3.9 21.1 - - - -
196B GLY 5.0 0.2 + - - -
197B GLY 4.5 0.7 - - - -
198B PRO* 3.1 32.9 - - - +
209B LEU* 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.1 4.7 - - + -
28B PRO 5.5 0.7 - - - +
29B TRP* 2.9 16.8 + - - +
31B ALA* 5.0 0.4 - - - +
45B SER* 1.3 69.6 - - - +
47B MET* 1.3 59.9 + - - +
48B SER 3.0 25.6 - - - +
49B PRO 3.8 12.3 - - - +
51B TRP 3.6 7.4 - - - +
52B VAL* 4.0 15.5 - - + +
68B LEU* 4.1 22.2 - - + -
108B ILE* 4.1 2.7 - - + -
112B ALA* 3.8 19.5 - - + -
118B ILE* 4.1 14.6 - - + -
119B GLN 3.8 19.5 - - - +
120B THR* 3.3 15.4 - - + -
121B ILE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A CYS* 5.8 0.5 - - - +
45B SER* 4.0 2.0 - - - +
46B LEU* 1.3 75.3 - - - +
48B SER* 1.3 65.7 - - - +
51B TRP* 2.9 15.8 + - + +
52B VAL 4.8 0.4 - - - -
53B ILE* 3.3 45.3 - - + +
105B LEU* 5.5 2.5 - - + -
120B THR* 3.8 11.8 - - - -
121B ILE* 3.2 44.5 - - + +
122B CYS 4.4 2.5 - - - -
123B LEU* 3.0 45.8 - - + +
209B LEU* 3.8 7.6 - - + -
238B ILE* 6.0 5.2 - - + -
242B THR* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.0 17.7 - - - +
47B MET* 1.3 78.4 - - - +
49B PRO* 1.3 79.8 - - - +
50B CYS 3.1 2.5 + - - -
51B TRP* 3.2 37.0 + - - +
120B THR* 3.8 10.5 - - - -
242B THR* 4.3 9.0 - - - +
----------------------------------------------------------
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