Contacts of the strand formed by residues 8 - 18 (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 VAL 8 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.0 22.0 - - + -
13C TYR 3.9 2.5 - - - -
14C GLN* 3.6 14.6 - - + +
70C LEU* 3.9 7.2 - - - +
82C ALA* 4.4 3.6 - - + -
113C PHE* 3.7 28.7 - - + -
114C PRO* 3.8 14.4 - - + -
115C PRO* 4.3 1.6 - - + -
6D ASP* 3.4 25.6 - - - +
7D PHE* 1.3 73.4 - - - +
9D TYR* 1.3 62.6 + - - +
10D GLN* 4.1 8.7 - - + +
32D TYR* 3.8 3.1 - - - -
33D ASN* 2.7 42.3 + - - +
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Residues in contact with TYR 9 (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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12C LEU* 3.7 3.8 - - - +
13C TYR 2.9 36.6 + - - +
66C LEU* 3.8 39.2 - - + +
69C ASN* 3.0 34.7 + - + -
70C LEU* 3.6 35.7 - - + -
73C VAL* 3.7 14.8 - - + -
8D VAL* 1.3 74.3 - - - +
10D GLN* 1.3 93.6 + - - +
11D PHE* 4.7 2.9 - - + -
30D TYR* 3.7 11.7 - + - -
31D ILE 3.6 6.1 - - - -
32D TYR* 4.8 3.1 - + - -
37D TYR* 2.5 37.8 + + - -
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Residues in contact with GLN 10 (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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10C VAL* 5.5 2.1 - - - +
11C ASN 3.5 6.7 - - - +
12C LEU* 4.2 7.9 - - + -
113C PHE* 3.6 10.9 - - - -
143C HIS* 3.0 28.8 + - - +
145C PHE* 3.1 24.4 - - + -
8D VAL* 4.1 7.6 - - + -
9D TYR* 1.3 88.8 - - - +
11D PHE* 1.3 59.6 + - - +
12D LYS* 3.7 21.7 - - + -
29D ARG 3.5 2.8 - - - +
30D TYR* 3.7 1.7 - - - -
31D ILE* 2.9 53.8 + - + +
33D ASN 3.0 23.8 + - - +
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Residues in contact with PHE 11 (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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9C GLY* 3.0 4.9 - - - +
10C VAL* 3.7 0.5 - - - -
11C ASN* 2.7 76.8 + - + -
62C ASN* 4.9 9.0 - - - -
66C LEU* 3.8 16.6 - - + +
9D TYR* 4.5 2.6 - - + -
10D GLN* 1.3 75.2 - - - +
12D LYS* 1.3 60.9 + - - +
13D GLY* 4.2 13.0 - - - -
28D THR* 3.9 25.8 - - + -
29D ARG 3.3 12.1 - - - -
30D TYR* 3.3 50.0 - + - -
74D GLU* 6.1 0.9 - - - -
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Residues in contact with LYS 12 (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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8C SER* 4.8 3.8 - - - +
9C GLY 3.4 4.0 - - - -
10C VAL* 4.9 11.4 - - + -
11C ASN 5.8 0.2 - - - +
139C SER* 3.9 22.6 - - - +
140C LYS 2.8 31.9 + - - -
141C SER* 4.5 2.4 - - - +
143C HIS* 3.1 35.6 + - + +
145C PHE* 6.0 0.2 - - - -
10D GLN* 3.7 20.6 - - + +
11D PHE* 1.3 78.7 - - - +
13D GLY* 1.3 59.6 + - - +
14D MET* 3.3 31.8 + - + +
27D VAL 3.4 3.5 - - - +
28D THR* 4.5 0.2 - - - -
29D ARG* 3.0 38.9 + - + +
31D ILE* 4.0 10.3 - - + -
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Residues in contact with GLY 13 (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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8C SER* 3.4 0.4 + - - -
9C GLY* 2.6 60.4 + - - +
11D PHE* 3.9 12.0 + - - -
12D LYS* 1.3 68.9 - - - +
14D MET* 1.3 56.7 + - - +
15D CYS* 5.4 0.8 - - - -
28D THR* 4.2 16.6 - - - -
78D VAL* 6.5 0.7 - - - -
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Residues in contact with MET 14 (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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6C VAL* 4.0 21.3 - - + -
7C ALA 3.1 5.6 - - - +
8C SER* 3.3 24.2 - - - +
141C SER* 6.3 3.6 - - - -
12D LYS* 3.7 29.4 - - + +
13D GLY* 1.3 74.4 - - - -
15D CYS* 1.3 61.0 + - - +
16D TYR* 3.4 25.6 - - + +
26D LEU* 3.3 5.9 - - - +
27D VAL 2.8 42.1 + - - +
28D THR* 4.8 1.0 - - - +
29D ARG* 3.5 27.6 - - - +
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Residues in contact with CYS 15 (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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5C HIS 3.8 1.0 - - - +
6C VAL* 3.6 3.1 - - - +
7C ALA* 2.7 36.4 + - + +
9C TYR* 3.7 21.3 - - + -
13D GLY 4.2 0.6 + - - -
14D MET* 1.3 75.7 - - - +
16D TYR* 1.3 63.9 + - - +
17D PHE* 3.6 22.9 - - + -
25D ARG 3.5 3.6 - - - -
26D LEU* 4.7 0.4 - - - -
78D VAL* 4.5 5.2 - - - -
79D CYS* 2.1 56.5 - - - -
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Residues in contact with TYR 16 (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* 3.9 3.1 - - + +
1C ILE* 3.8 37.2 - - + -
3C ALA* 3.9 12.3 - - + -
5C HIS 3.5 2.9 - - - -
6C VAL* 3.8 34.3 - - + -
14D MET* 3.4 32.9 - - + +
15D CYS* 1.3 73.6 - - - +
17D PHE* 1.3 62.6 + - - +
23D ARG 3.7 0.9 - - - +
24D VAL* 3.4 8.0 - - - +
25D ARG* 2.7 57.4 + - + +
27D VAL* 3.9 26.5 - - + -
29D ARG* 2.7 27.7 + - - -
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Residues in contact with PHE 17 (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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3C ALA* 3.4 0.9 - - - +
4C ASP* 2.9 21.0 + - - +
5C HIS* 3.0 39.8 + - + +
7C ALA* 4.4 6.1 - - + -
9C TYR* 4.3 18.2 - + - -
26C PHE* 4.6 4.0 - + - -
15D CYS* 3.6 30.7 - - + -
16D TYR* 1.3 72.8 - - - +
18D THR* 1.3 68.4 + - - +
20D GLY 3.8 8.3 - - - +
21D THR* 4.4 4.7 - - + -
23D ARG 3.6 3.1 - - - -
24D VAL* 3.8 33.4 - - + -
79D CYS* 3.8 18.8 - - - -
83D TYR* 3.6 44.6 - + + -
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Residues in contact with THR 18 (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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3C ALA* 3.4 17.4 - - - +
4C ASP* 3.3 21.1 + - - +
17D PHE* 1.3 82.0 + - - +
19D ASN* 1.3 76.7 + - + +
20D GLY 3.0 9.6 + - - +
23D ARG* 2.9 43.6 + - + +
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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