Contacts of the strand formed by residues 23 - 32 (chain D) in PDB entry 4GG6
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 ARG 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D TYR 3.7 1.0 - - - +
17D PHE* 3.6 4.0 - - - -
18D THR* 2.9 51.2 + - + +
19D ASN* 5.7 0.9 - - + -
20D GLY 4.5 0.2 - - - +
22D GLU* 1.3 77.4 - - + +
24D VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TYR 3.4 4.9 - - - +
17D PHE* 3.8 16.4 - - + -
21D THR* 3.3 44.4 - - + +
22D GLU 4.1 0.8 + - - -
23D ARG* 1.3 75.9 - - - +
25D ARG* 1.3 67.7 + - - +
42D SER* 4.8 0.5 + - - -
43D ASP* 4.8 4.3 - - - +
75D LEU* 3.8 20.0 - - + +
79D CYS* 3.8 30.7 - - + -
80D ARG* 4.6 22.0 - - + +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C ASP 3.6 33.9 + - - +
1C ILE* 4.2 12.0 - - - +
15D CYS* 3.5 1.2 - - - -
16D TYR* 2.7 51.2 + - + +
24D VAL* 1.3 77.6 - - - +
26D LEU* 1.3 64.1 + - - +
27D VAL* 4.3 7.7 - - + +
41D ASP* 3.0 36.8 + - - +
42D SER* 3.4 13.9 - - - +
43D ASP* 3.4 28.0 + - - +
75D LEU* 4.1 4.7 - - - -
79D CYS* 4.3 0.7 - - - -
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D MET 3.3 7.4 - - - +
15D CYS* 4.7 0.4 - - - -
25D ARG* 1.3 73.3 - - - +
27D VAL* 1.3 72.0 + - - +
28D THR* 3.9 25.1 - - + -
40D PHE* 3.9 21.1 - - + -
41D ASP* 3.5 0.5 - - - +
42D SER* 2.8 44.0 + - - -
71D THR* 3.8 14.1 - - + +
72D ARG 4.5 0.4 - - - +
74D GLU* 3.6 10.3 - - + +
75D LEU* 3.3 43.4 - - + +
79D CYS* 3.6 17.7 - - - -
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Residues in contact with VAL 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C ASP 4.8 2.9 - - - +
12D LYS 3.4 3.5 - - - +
14D MET* 2.8 36.2 + - - +
16D TYR* 3.9 21.0 - - + -
25D ARG* 4.3 13.0 - - - +
26D LEU* 1.3 80.9 - - - +
28D THR* 1.3 63.8 + - - +
29D ARG* 3.5 41.3 + - + +
39D ARG* 3.9 13.9 - - - -
40D PHE 3.3 9.0 - - - +
41D ASP* 3.7 23.6 - - + +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.9 28.7 - - + -
12D LYS 3.5 3.6 - - - -
13D GLY* 4.2 9.6 - - - -
14D MET 4.8 0.9 - - - +
26D LEU* 3.9 17.3 - - + -
27D VAL* 1.3 74.3 - - - +
29D ARG* 1.3 62.5 + - - +
30D TYR* 3.7 10.9 + - - -
39D ARG* 3.3 6.9 - - - +
40D PHE* 3.0 44.2 + - - +
71D THR* 4.4 6.1 - - + +
74D GLU* 4.8 11.9 - - - +
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Residues in contact with ARG 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C ASP* 3.1 37.1 - - - +
143C HIS* 4.2 14.8 - - - -
10D GLN 3.5 1.7 - - - +
11D PHE* 3.3 8.8 - - - -
12D LYS* 3.0 39.0 + - + +
14D MET* 3.5 23.0 - - - +
16D TYR* 2.7 24.9 + - - -
27D VAL* 3.5 17.8 - - + +
28D THR* 1.3 75.0 - - - +
30D TYR* 1.3 62.3 + - - +
31D ILE* 3.8 11.7 - - + +
36D GLU* 3.3 34.6 + - - +
39D ARG* 3.4 30.9 - - - +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 4.4 7.2 - - - -
9D TYR* 3.7 17.0 - + - +
10D GLN 3.7 3.1 - - - -
11D PHE* 3.3 38.1 - + - -
28D THR* 3.7 15.4 + - - -
29D ARG* 1.3 73.4 - - - +
31D ILE* 1.3 61.8 + - - +
36D GLU* 3.3 6.2 - - - +
37D TYR* 3.0 46.0 + - + +
38D ALA* 3.1 22.2 + - + +
47D TYR* 3.4 39.8 + + - -
61D TRP* 3.8 28.0 - + - -
71D THR* 5.5 0.2 - - - +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C HIS* 3.4 34.5 - - + +
9D TYR* 3.6 8.1 - - - -
10D GLN* 2.9 50.6 + - + +
12D LYS* 4.0 14.1 - - + -
29D ARG* 3.8 24.0 - - + +
30D TYR* 1.3 79.2 - - - +
32D TYR* 1.3 59.0 + - - +
33D ASN 3.2 23.0 + - - +
34D ARG* 3.6 9.4 - - - +
35D GLU 3.2 20.6 - - - +
36D GLU* 3.8 16.6 - - + -
37D TYR* 3.9 5.3 - - - -
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 3.8 15.5 - - + -
73C VAL* 3.5 31.4 - - + -
74C ILE* 3.3 30.2 - - + +
77C SER* 3.1 35.4 + - - -
80C THR* 2.7 32.7 + - + -
7D PHE* 3.2 17.5 - + + -
8D VAL 3.9 6.3 - - - -
9D TYR* 4.8 2.0 - + - -
31D ILE* 1.3 68.7 - - - +
33D ASN* 1.3 84.5 + - - +
34D ARG 2.9 0.7 + - - -
35D GLU* 2.7 35.7 + - + +
37D TYR* 3.7 5.4 - - + -
53D LEU* 3.9 15.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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