Contacts of the strand formed by residues 34 - 45 (chain A) in PDB entry 2G98
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 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 2.9 29.5 + - - +
8A ASP 2.7 21.5 + - - -
11A PHE* 2.9 28.2 + - - -
32A CYS* 3.4 9.8 - - - -
33A ASN* 1.3 79.9 - - - +
35A ALA* 1.3 59.4 + - - +
62A TYR 3.1 19.3 - - - -
63A ALA* 3.5 13.0 - - - -
68A TRP* 3.9 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.4 2.9 - - + -
4A THR 3.3 6.1 - - - +
5A LEU* 3.8 22.9 - - + -
6A TYR* 4.5 0.9 - - - -
11A PHE* 3.5 4.0 - - - -
34A SER* 1.3 76.6 - - - +
36A SER* 1.3 65.5 + - - +
37A VAL 4.2 0.2 - - - -
57A LEU* 4.0 19.5 - - + -
62A TYR* 3.0 32.1 + - + +
68A TRP* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.3 4.4 - - - -
4A THR* 2.7 45.1 + - - -
6A TYR* 4.4 2.6 - - - -
11A PHE* 3.4 10.0 - - - -
35A ALA* 1.3 71.4 - - - +
37A VAL* 1.4 64.1 + - - +
38A ASP* 3.7 2.2 + - - +
60A GLY 3.7 3.6 - - - -
61A ASP* 2.5 26.9 + - - -
24B ASN* 2.9 28.2 + - - -
27B PRO* 5.1 5.4 - - - -
28B TYR* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS 3.9 2.9 - - - +
3A ILE* 3.8 26.2 - - + -
35A ALA 4.2 0.2 - - - -
36A SER* 1.4 68.6 - - - +
38A ASP* 1.3 63.6 + - - +
39A SER 3.7 12.6 - - - +
40A GLY 3.5 24.7 - - - +
42A TRP* 3.9 9.4 - - + -
57A LEU* 4.1 18.2 - - + -
58A ARG 3.3 21.8 - - - +
59A ARG* 3.6 14.8 + - - +
60A GLY 2.8 27.8 + - - +
62A TYR* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 2.9 35.5 + - + +
4A THR* 6.1 0.9 - - - +
36A SER 3.7 4.3 + - - +
37A VAL* 1.3 74.3 - - - +
39A SER* 1.4 80.5 + - - +
59A ARG* 3.0 31.0 + - - +
27B PRO* 6.4 1.1 - - + -
28B TYR* 2.5 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 3.8 10.2 + - - -
2A LYS* 3.2 24.8 + - - +
37A VAL* 3.5 3.0 - - - +
38A ASP* 1.4 91.0 + - - +
40A GLY* 1.3 63.6 + - - +
42A TRP* 3.1 20.4 + - - -
59A ARG* 4.8 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 4.2 3.8 - - - -
37A VAL* 3.5 14.6 - - - +
39A SER* 1.3 80.0 - - - +
41A CYS* 1.3 65.3 + - - -
42A TRP* 3.9 2.5 - - - -
59A ARG* 3.8 12.4 + - - +
80A LEU* 4.1 12.8 - - - -
171A ASP* 3.4 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY* 1.3 76.7 - - - -
42A TRP* 1.3 60.9 + - - +
56A PHE* 3.9 16.6 - - + -
57A LEU 3.6 4.7 - - - -
58A ARG* 4.6 9.4 - - - -
80A LEU* 3.6 7.5 - - - +
81A ILE* 2.9 30.9 + - + +
169A VAL* 3.4 32.8 - - + -
170A ILE 3.3 26.5 - - - -
171A ASP* 3.6 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 3.7 5.6 - - - -
2A LYS 3.6 25.0 + - - -
3A ILE* 3.7 35.0 - - + -
18A CYS* 3.5 28.9 - - + -
19A SER 3.9 0.9 - - - -
20A SER 3.7 24.5 - - - -
37A VAL* 3.9 24.9 - - + -
39A SER 3.1 19.6 + - - -
40A GLY 3.9 1.1 - - - -
41A CYS* 1.3 76.7 - - - +
43A MET* 1.3 62.9 + - - +
44A LEU* 4.2 3.4 - - + -
55A TYR 3.7 0.7 - - - +
56A PHE* 3.5 6.4 - - - -
57A LEU* 2.9 39.0 + - + +
78A CYS* 4.2 12.8 - - + -
79A ARG 3.3 21.3 - - - -
80A LEU* 3.7 29.0 - - + +
81A ILE* 3.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 1.3 74.1 - - - +
44A LEU* 1.4 63.2 + - - +
45A TYR* 3.6 28.8 - - + +
54A GLN* 3.6 36.1 - - + +
55A TYR 3.4 1.6 - - - -
56A PHE* 3.8 32.1 - - - +
78A CYS* 3.2 6.4 - - - +
79A ARG* 2.9 35.1 + - + -
81A ILE* 3.9 16.8 - - + +
131A VAL* 4.0 11.9 - - + -
142A GLN* 3.9 14.4 - - + +
144A LEU* 3.9 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.2 21.3 - - + -
5A LEU* 4.2 11.9 - - + -
42A TRP* 4.9 2.5 - - + -
43A MET* 1.4 74.6 - - - +
45A TYR* 1.3 61.1 + - - +
53A LEU 3.8 0.3 - - - +
54A GLN* 3.2 5.4 - - - +
55A TYR* 2.8 45.4 + - + +
57A LEU* 3.8 34.1 - - + -
68A TRP* 4.0 24.9 - - + -
75A VAL* 4.0 29.4 - - + -
77A SER 3.9 2.0 - - - -
78A CYS* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 3.6 35.1 - - + +
44A LEU* 1.3 77.0 - - - +
46A GLU* 1.3 61.2 + - - +
47A GLN 3.4 0.2 + - - -
50A TYR* 3.4 48.7 - + + -
51A SER 3.5 12.3 - - - +
53A LEU 3.4 2.7 - - - -
54A GLN* 3.5 40.5 + - + -
55A TYR* 5.6 1.1 - - - -
74A SER 4.6 0.2 - - - -
75A VAL* 3.5 5.4 - - - -
76A ARG 2.9 25.5 + - - -
77A SER* 3.0 28.0 + - - +
79A ARG* 3.2 34.3 + - + -
144A LEU* 3.9 6.6 - - - +
----------------------------------------------------------
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