Contacts of the strand formed by residues 5 - 14 (chain C) 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 HIS 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ALA* 3.2 1.2 + - - +
4C ASP* 1.3 103.3 + - + +
6C VAL* 1.3 64.2 + - - +
26C PHE* 3.6 20.3 - + + -
27C ASP* 2.9 31.3 + - - +
16D TYR* 3.5 4.0 - - - -
17D PHE* 3.0 50.2 + - + -
83D TYR* 4.9 11.2 + + - -
91D LEU* 3.8 25.8 - - + +
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Residues in contact with VAL 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ILE 4.9 4.7 - - - +
2C VAL* 5.8 0.2 - - - -
3C ALA 4.3 17.0 - - - +
5C HIS* 1.3 75.7 - - - +
7C ALA* 1.3 63.7 + - - +
27C ASP* 2.8 36.4 + - - +
28C GLY 4.5 0.7 + - - -
14D MET* 4.0 20.2 - - + -
15D CYS 3.6 3.4 - - - +
16D TYR* 3.8 36.3 - - + -
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Residues in contact with ALA 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 1.3 79.1 - - - +
8C SER* 1.3 61.9 + - - +
9C TYR* 3.6 34.5 + - + +
25C GLU 3.6 10.3 - - - +
26C PHE* 3.7 16.4 - - + +
14D MET* 3.1 6.3 - - - +
15D CYS 2.7 41.8 + - - +
17D PHE* 4.4 4.0 - - + -
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Residues in contact with SER 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 1.3 69.3 - - - +
9C TYR* 1.3 68.9 + - - +
10C VAL* 3.5 31.5 - - - +
24C HIS* 3.4 2.4 - - - +
25C GLU* 2.9 46.4 + - - +
139C SER* 4.3 3.1 + - - -
12D LYS* 4.8 2.6 - - - +
13D GLY 3.5 6.3 - - - -
14D MET* 3.3 27.2 - - - +
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Residues in contact with TYR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 3.6 22.5 + - + +
8C SER* 1.3 72.1 - - - +
9C GLY* 1.3 56.1 + - - +
22C TYR* 4.0 3.5 + - - -
24C HIS* 3.4 29.8 + + + -
25C GLU 4.3 4.9 - - - -
26C PHE* 3.6 8.7 - - - -
31C GLU* 4.2 8.1 - - - -
52C ARG* 4.8 0.7 - - - -
11D PHE* 5.9 0.9 - - - -
13D GLY* 2.6 21.4 + - - +
15D CYS* 3.7 31.9 - - + -
17D PHE* 4.3 8.0 - + - -
78D VAL* 3.8 22.7 - - + +
82D ASN* 3.2 39.9 - - + +
86D GLU* 2.7 43.8 + - - +
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Residues in contact with GLY 9 (chain C).
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 3.1 6.9 + - - -
9C TYR* 1.3 75.6 - - - +
10C VAL* 1.3 59.3 + - - +
11C ASN* 3.0 18.4 + - - +
22C TYR* 3.7 9.2 - - - -
23C SER 3.8 0.7 - - - -
24C HIS* 3.1 15.6 - - - -
11D PHE* 3.0 7.5 - - - +
12D LYS* 3.4 1.2 - - - -
13D GLY 2.8 27.5 + - - +
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Residues in contact with VAL 10 (chain C).
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* 3.5 25.1 - - - +
9C GLY* 1.3 68.9 - - - +
11C ASN* 1.3 63.8 + - - +
12C LEU* 5.2 3.1 - - + -
21C GLN* 3.2 21.5 - - - +
22C TYR* 3.6 0.9 - - - -
23C SER* 2.8 38.2 + - - +
25C GLU* 3.9 11.4 - - - +
137C PHE 5.2 1.1 - - - +
139C SER* 3.5 35.0 - - - +
145C PHE* 4.6 15.5 - - + -
10D GLN* 5.5 1.1 - - - +
11D PHE 3.7 2.7 - - - +
12D LYS* 4.8 11.7 - - + +
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Residues in contact with ASN 11 (chain C).
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 29.9 + - - +
10C VAL* 1.3 73.3 - - - +
12C LEU* 1.3 60.3 + - - +
21C GLN 3.6 3.6 - - - -
22C TYR* 2.9 27.4 - - + -
62C ASN* 2.9 22.7 + - - +
63C ILE* 4.7 1.9 - - + +
66C LEU* 3.5 20.6 - - + +
10D GLN* 3.5 6.4 - - - +
11D PHE* 2.7 65.2 + - + +
12D LYS* 5.8 0.2 - - - +
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Residues in contact with LEU 12 (chain C).
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* 4.9 5.6 - - + +
11C ASN* 1.3 75.0 - - - +
13C TYR* 1.3 73.7 + - - +
14C GLN* 5.0 6.7 - - - +
20C GLY* 2.9 6.4 - - - -
21C GLN* 2.8 62.7 + - + +
63C ILE* 3.4 7.3 - - - +
66C LEU* 3.5 3.2 - - - +
115C PRO* 3.7 36.1 - - + -
137C PHE* 4.8 2.9 - - + -
145C PHE* 3.9 25.1 - - + -
8D VAL* 4.0 14.1 - - + -
9D TYR 3.7 12.1 - - - +
10D GLN* 4.2 2.0 - - + -
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Residues in contact with TYR 13 (chain C).
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* 1.3 79.6 - - - +
14C GLN* 1.3 66.6 + - - +
15C SER* 4.7 1.9 - - - -
18C PRO* 3.5 32.2 - - + +
19C SER 3.3 21.5 - - - -
20C GLY 4.6 0.2 - - - -
63C ILE* 3.8 22.0 - - + -
66C LEU* 3.9 20.4 - - + -
67C LYS* 3.7 37.1 - - + +
70C LEU* 3.5 24.4 - - + +
9D TYR* 2.9 36.4 + - + +
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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