Contacts of the helix formed by residues 8 - 16 (chain D) in PDB entry 2GBK
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 LEU 8 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN* 5.3 5.2 - - + +
11B VAL* 3.5 34.8 - - + +
14B LEU* 6.0 5.6 - - + -
7D THR* 1.3 80.2 - - - +
9D THR* 1.3 61.2 + - - +
10D GLN* 3.3 22.7 - - - +
11D VAL* 3.2 19.2 + - + +
12D ARG* 2.9 26.0 + - - +
51D ILE* 4.9 6.7 - - + -
75D HIS* 4.2 24.7 - - + +
76D LEU 4.2 1.0 + - - -
77D VAL* 3.7 24.0 - - + -
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Residues in contact with THR 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR 3.8 0.8 + - - -
8D LEU* 1.3 73.0 - - - +
10D GLN* 1.3 58.8 + - - +
12D ARG* 3.8 6.0 - - + +
13D GLU* 2.8 43.0 + - + +
75D HIS* 5.1 9.3 - - - -
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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
----------------------------------------------------------
8B LEU* 3.9 27.5 - - + +
10B GLN* 2.9 51.6 + - - +
11B VAL* 6.0 0.2 - - - -
8D LEU* 4.3 15.7 - - + +
9D THR* 1.3 78.6 - - - +
11D VAL* 1.3 68.1 + - + +
13D GLU* 4.3 5.3 - - - +
14D LEU* 3.4 22.9 + - - +
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 25.4 - - + -
11B VAL* 5.5 2.2 - - + -
77B VAL* 3.8 25.4 - - + -
78B LEU 3.3 28.3 - - - +
7D THR* 4.0 13.5 - - - +
8D LEU* 3.2 30.2 + - + +
10D GLN* 1.3 78.5 - - + +
12D ARG* 1.3 58.4 + - - +
14D LEU* 3.2 5.7 + - - +
15D VAL* 2.9 29.6 + - + +
16D GLY 5.4 0.2 - - - +
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Residues in contact with ARG 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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78B LEU 5.0 0.4 + - - -
80B LEU* 3.7 12.3 - - - +
49C ARG* 5.5 3.1 + - - -
79C ARG* 5.5 0.2 + - - -
6D LYS* 3.4 24.9 - - - +
7D THR* 3.0 49.5 + - - +
8D LEU 2.9 17.3 + - - +
9D THR* 3.8 7.0 - - + +
11D VAL* 1.3 74.3 - - - +
13D GLU* 1.3 60.2 + - + +
16D GLY* 2.9 49.7 + - - -
17D GLY* 3.4 31.8 + - - +
18D LYS 2.8 31.0 + - - +
19D THR* 3.8 1.0 - - - +
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Residues in contact with GLU 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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15A VAL 5.0 3.3 - - - +
18A LYS* 5.0 1.6 - - - -
49C ARG* 3.4 24.0 + - - +
56C GLN* 5.7 3.1 + - - -
79C ARG* 3.1 47.5 + - - +
81C ARG* 5.6 0.2 - - - +
9D THR* 2.8 33.6 + - + +
10D GLN* 4.3 5.8 - - - +
12D ARG* 1.3 78.5 - - + +
14D LEU* 1.3 62.4 + - - +
16D GLY 4.7 0.5 + - - -
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Residues in contact with LEU 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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18A LYS* 2.7 50.2 + - - +
8B LEU* 5.9 5.6 - - + -
51B ILE* 3.5 39.7 - - + -
54B GLY 4.7 6.5 - - - +
56B GLN* 5.6 2.2 - - + +
77B VAL* 5.0 11.7 - - + -
81C ARG* 3.3 8.5 - - - +
10D GLN 3.4 17.7 + - - +
11D VAL* 3.2 5.7 + - - +
13D GLU* 1.3 81.6 - - - +
15D VAL* 1.3 72.7 + - + +
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Residues in contact with VAL 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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49B ARG* 3.8 33.6 + - + -
51B ILE* 6.4 0.4 - - + -
56B GLN* 3.8 23.7 - - + +
77B VAL* 4.0 12.1 - - + -
78B LEU 3.6 23.1 - - - +
79B ARG* 3.5 14.3 + - + +
81C ARG* 3.5 17.6 - - - -
11D VAL* 2.9 23.4 + - + +
14D LEU* 1.3 91.9 - - + +
16D GLY* 1.3 67.7 + - - +
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Residues in contact with GLY 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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78B LEU 4.7 0.3 - - - +
79B ARG* 3.6 5.8 - - - -
46C ASP* 3.5 14.4 - - - -
81C ARG* 4.3 5.8 - - - +
7D THR* 4.8 0.3 + - - -
12D ARG* 2.9 43.1 + - - -
13D GLU 4.6 0.6 + - - -
14D LEU 3.7 1.0 - - - -
15D VAL* 1.3 89.5 - - - +
17D GLY* 1.3 57.2 + - - -
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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