Contacts of the helix formed by residues 10 - 22 (chain C) 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 GLN 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C GLY* 1.3 69.9 - - - +
11C LEU* 1.3 56.6 + - + +
12C ALA 2.6 12.5 + - - -
13C PHE* 2.8 22.9 + - - +
14C ALA* 3.5 3.0 + - - +
40C ALA* 5.4 4.3 - - - +
41C THR* 2.5 36.8 + - - +
124C THR* 6.4 0.2 - - - -
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Residues in contact with LEU 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 3.2 0.4 + - - -
10C GLN* 1.3 77.5 - - + +
12C ALA* 1.3 51.4 + - - +
14C ALA* 3.5 19.5 - - + -
15C LEU* 2.7 46.6 + - + +
69C ALA* 6.0 2.9 - - + -
95C CYS 6.1 1.3 - - - +
121C MET* 5.9 2.0 - - + -
122C THR* 4.0 29.8 - - - +
123C ASN 3.5 9.4 - - - +
124C THR* 3.5 37.4 - - + +
126C VAL* 3.7 4.7 - - + -
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Residues in contact with ALA 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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5C PHE* 3.6 27.8 - - + -
7C GLY 3.2 17.0 - - - +
8C ALA* 3.8 1.8 - - - -
9C GLY 2.7 37.2 + - - +
10C GLN 2.6 5.7 + - - -
11C LEU* 1.3 71.0 - - - +
13C PHE* 1.3 63.4 + - - +
15C LEU* 3.3 5.4 + - - +
16C ALA* 3.0 22.4 + - - +
45C LEU* 5.0 4.3 - - + -
69C ALA* 5.2 2.4 - - + +
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Residues in contact with PHE 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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9C GLY 3.9 0.2 + - - -
10C GLN 2.8 10.6 + - - +
12C ALA* 1.3 80.4 - - - +
14C ALA* 1.3 63.9 + - - +
16C ALA* 3.4 6.1 - - + +
17C LYS* 3.1 56.8 + - + +
40C ALA 5.7 0.2 - - - -
41C THR* 3.9 31.4 - - + +
44C ALA* 3.7 25.1 - - + -
45C LEU* 3.4 49.6 - - + +
48C MET* 4.4 13.2 - - + -
127C VAL* 6.4 0.4 - - + -
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Residues in contact with ALA 14 (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 GLN 3.5 2.5 + - - +
11C LEU* 3.5 31.0 - - + +
12C ALA 3.2 0.2 - - - -
13C PHE* 1.3 81.1 - - - +
15C LEU* 1.3 67.8 + - - +
17C LYS* 3.2 4.5 + - - +
18C GLY* 2.9 19.2 + - - -
124C THR* 5.0 2.0 - - + -
126C VAL* 3.9 6.3 - - + -
127C VAL* 3.2 41.7 - - + +
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Residues in contact with LEU 15 (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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5C PHE* 3.5 26.9 - - + -
11C LEU* 2.7 30.5 - - + +
12C ALA* 3.4 5.2 - - - +
14C ALA* 1.3 78.0 - - - +
16C ALA* 1.3 67.9 + - - +
18C GLY* 2.7 15.1 + - - -
19C PHE* 2.7 35.8 - - + -
67C PHE* 5.2 12.6 - - + -
69C ALA* 5.0 10.5 - - + -
95C CYS* 6.6 0.2 - - - -
122C THR* 4.4 16.4 - - + +
126C VAL* 4.3 21.3 - - + +
153C LEU* 5.0 9.2 - - + -
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Residues in contact with ALA 16 (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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5C PHE* 4.4 7.5 - - + -
12C ALA 3.0 9.6 + - - +
13C PHE* 3.4 15.0 - - + +
15C LEU* 1.3 82.8 - - - +
17C LYS* 1.3 56.9 + - - +
18C GLY 2.7 8.1 + - - -
19C PHE* 3.0 18.4 + - - +
20C THR* 2.8 16.1 + - - +
45C LEU* 5.6 5.4 - - + -
48C MET* 5.2 11.9 - - + -
50C VAL* 5.3 9.4 - - + -
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Residues in contact with LYS 17 (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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13C PHE* 3.1 43.0 + - + +
14C ALA* 3.5 7.9 - - - +
16C ALA* 1.3 77.9 - - - +
18C GLY* 1.3 55.5 + - - +
20C THR* 3.0 11.8 + - + -
21C ALA* 3.0 32.8 + - + +
48C MET* 4.8 13.1 - - - -
127C VAL* 3.5 36.0 - - + +
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Residues in contact with GLY 18 (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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14C ALA 2.9 8.6 + - - -
15C LEU 2.7 16.8 + - - -
17C LYS* 1.3 69.6 - - - +
19C PHE* 1.3 54.0 + - - -
20C THR 2.8 1.6 + - - -
21C ALA* 3.2 2.7 + - - +
22C ALA* 2.6 38.2 + - - +
126C VAL 4.1 15.9 - - - -
127C VAL 5.3 3.4 - - - -
128C VAL 6.2 0.4 - - - -
156C VAL* 4.3 12.1 - - - +
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Residues in contact with PHE 19 (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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3C VAL* 6.3 1.3 - - + -
5C PHE* 4.5 10.3 - + - -
15C LEU* 2.7 54.1 - - + -
16C ALA* 3.0 9.2 + - - +
18C GLY* 1.3 72.1 - - - +
20C THR* 1.3 67.3 + - - +
22C ALA* 3.0 20.5 - - - +
24C VAL* 3.2 16.3 + - + +
25C LEU* 3.6 39.3 + - + -
67C PHE* 4.7 13.0 - + - -
152C LEU* 3.4 40.6 - - + -
153C LEU* 3.5 28.0 - - + -
155C SER* 5.2 0.2 - - - -
156C VAL* 4.5 7.7 - - + +
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Residues in contact with THR 20 (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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16C ALA* 2.8 17.7 + - - +
17C LYS* 3.0 17.1 + - + -
18C GLY 2.8 0.4 + - - -
19C PHE* 1.3 75.9 - - - +
21C ALA* 1.3 55.2 + - - +
23C GLY* 2.5 31.9 + - - -
24C VAL 3.9 0.3 + - - -
25C LEU* 4.3 15.6 - - - +
27C ALA* 5.5 6.7 + - + +
48C MET* 4.0 29.3 - - + +
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Residues in contact with ALA 21 (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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17C LYS* 3.0 16.9 + - + +
18C GLY* 4.0 2.0 - - - +
20C THR* 1.3 75.0 - - + +
22C ALA* 1.3 57.8 + - - +
23C GLY* 2.7 13.2 + - - -
127C VAL 6.1 0.4 - - - +
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Residues in contact with ALA 22 (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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18C GLY 2.6 23.9 + - - +
19C PHE* 3.0 18.6 - - - +
21C ALA* 1.3 72.3 - - - +
23C GLY* 1.3 58.7 + - - +
24C VAL* 2.9 26.3 - - + +
155C SER* 4.0 27.5 - - - +
156C VAL* 4.5 1.1 - - + -
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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