Contacts of the helix formed by residues 9 - 18 (chain B) in PDB entry 2GRA
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 GLY 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ALA* 1.3 74.6 - - - +
10B GLN* 1.3 78.4 + - - +
12B ALA* 3.5 5.5 - - - +
13B PHE* 2.8 23.3 - - - +
38B ASP* 5.3 3.1 - - - -
41B THR* 3.3 22.2 + - - +
42B VAL* 4.7 6.0 - - - +
45B LEU* 4.4 6.5 - - - +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ALA 3.9 3.2 + - - -
9B GLY* 1.3 84.6 - - - +
11B LEU* 1.3 61.7 + - + +
12B ALA 2.6 16.2 + - - +
13B PHE* 2.7 9.7 + - - +
14B ALA* 3.3 7.7 + - - +
38B ASP* 5.4 3.1 - - - +
41B THR* 5.1 2.8 + - - -
69B ALA 5.9 0.4 + - - -
124B THR* 6.4 1.8 - - - -
127B VAL* 5.7 0.3 - - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.2 1.1 - - - -
10B GLN* 1.3 82.6 - - + +
12B ALA* 1.3 60.0 + - - +
14B ALA* 3.5 9.1 - - + +
15B LEU* 2.8 41.2 + - + +
69B ALA* 4.7 11.8 - - + +
95B CYS* 4.1 25.4 - - + +
96B ALA* 5.2 4.7 - - + -
122B THR* 3.8 16.6 - - - +
123B ASN* 3.6 29.6 - - - +
124B THR* 4.7 5.4 - - + +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.1 20.7 - - + -
7B GLY 3.0 30.1 - - - +
8B ALA* 3.3 19.1 - - - -
9B GLY 3.5 3.8 - - - +
10B GLN 2.6 6.3 + - - -
11B LEU* 1.3 73.6 - - - +
13B PHE* 1.3 53.8 + - - +
14B ALA 3.1 0.3 + - - -
16B ALA* 2.6 41.1 + - - +
32B ALA* 6.1 1.1 - - + -
45B LEU* 5.3 4.3 - - + -
69B ALA* 4.2 3.3 - - + +
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Residues in contact with PHE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY 2.8 20.7 + - - +
10B GLN* 2.7 7.6 + - - +
12B ALA* 1.3 74.6 - - - +
14B ALA* 1.3 52.9 + - - +
16B ALA* 3.0 5.8 - - - +
17B LYS* 2.7 73.6 + - - +
40B ALA 5.9 0.4 - - - -
41B THR* 3.5 29.4 - - + -
44B ALA* 6.1 3.8 - - + -
45B LEU* 4.3 5.1 - - - +
48B MET* 3.6 28.0 - - + -
127B VAL* 5.4 7.6 - - + -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN 3.3 3.9 + - - +
11B LEU* 3.5 19.5 - - + +
12B ALA 3.0 0.8 - - - -
13B PHE* 1.3 76.2 - - - +
15B LEU* 1.3 57.6 + - + +
16B ALA 2.9 0.6 + - - -
17B LYS* 3.4 2.1 - - - +
18B GLY* 2.5 35.1 + - - -
123B ASN 4.8 4.5 - - - +
124B THR* 4.2 4.3 - - + +
126B VAL* 4.3 9.9 - - + -
127B VAL* 3.3 45.1 - - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.2 22.9 - - + -
11B LEU* 2.8 36.1 + - + +
14B ALA* 1.3 80.2 - - + +
16B ALA* 1.3 66.5 + - - +
18B GLY* 2.7 9.7 - - - +
19B PHE* 2.6 57.3 - - + -
67B PHE* 3.9 15.3 - - + -
69B ALA* 6.0 0.2 - - + -
95B CYS* 6.5 2.0 - - + -
122B THR* 5.8 8.3 - - + +
126B VAL* 4.6 15.2 - - + +
153B LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.1 9.1 - - + -
12B ALA 2.6 26.7 + - - +
13B PHE* 3.0 12.3 - - - +
14B ALA 2.9 0.4 + - - -
15B LEU* 1.3 79.1 - - - +
17B LYS* 1.3 52.2 + - - +
18B GLY 2.5 16.5 + - - +
19B PHE* 4.4 1.5 - - - -
20B THR* 2.7 16.3 - - - +
45B LEU* 5.2 2.2 - - + -
48B MET* 4.1 16.6 - - + -
50B VAL* 5.3 13.5 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 2.7 51.7 + - - +
14B ALA 3.7 2.2 - - - +
16B ALA* 1.3 72.7 - - - +
18B GLY* 1.3 56.5 + - - +
20B THR* 3.0 24.2 + - - +
22B ALA* 5.8 0.9 - - - +
48B MET* 4.0 12.9 - - + +
127B VAL* 3.5 38.6 - - + +
128B VAL 5.7 0.2 - - - +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.5 19.8 + - - -
15B LEU* 2.7 14.8 - - - +
16B ALA 2.5 20.0 + - - +
17B LYS* 1.3 72.0 - - - +
19B PHE* 1.3 56.8 + - - -
20B THR 2.4 20.8 + - - -
22B ALA* 5.1 0.7 - - - -
126B VAL 4.4 3.8 + - - -
127B VAL 5.2 0.9 - - - -
128B VAL 5.4 2.2 - - - -
156B VAL* 3.8 17.9 - - - -
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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