Contacts of the helix formed by residues 6 - 18 (chain C) in PDB entry 2AG1
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 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C THR* 1.3 72.1 - - - +
7C GLY* 1.3 56.4 + - - +
9C LEU* 3.1 7.5 + - - +
10C VAL* 2.9 31.0 + - - +
135C THR* 3.6 24.6 - - - +
138C ILE* 3.7 12.8 - - - +
165C ILE 4.0 1.3 - - - -
166C LEU* 2.9 17.5 + - - -
168C ASN 3.2 8.1 + - - -
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Residues in contact with GLY 7 (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 THR* 3.1 2.0 + - - -
6C GLY* 1.3 75.1 - - - +
8C GLU* 1.3 59.6 + - - +
10C VAL* 3.3 5.3 + - - +
11C VAL* 3.1 26.7 + - - +
32C THR* 3.3 35.1 + - - +
33C ILE* 4.0 11.0 - - - +
36C ALA* 3.9 0.4 - - - +
166C LEU* 3.2 13.6 + - - +
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Residues in contact with GLU 8 (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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4C ILE* 4.0 26.0 - - + -
5C THR* 2.9 24.7 + - + +
7C GLY* 1.3 70.6 - - - +
9C LEU* 1.3 58.6 + - - +
11C VAL* 3.1 2.6 + - - +
12C ARG* 2.5 79.3 + - - +
36C ALA* 3.3 30.0 - - + +
39C ASP* 4.7 6.8 - - - +
40C HIS* 3.3 23.5 + - - -
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Residues in contact with LEU 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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4C ILE* 3.5 23.3 - - + -
5C THR 3.1 4.4 + - - +
6C GLY* 3.1 12.3 + - - +
8C GLU* 1.3 79.3 - - - +
10C VAL* 1.3 62.4 + - - +
12C ARG* 4.0 4.2 - - - +
13C THR* 2.9 28.4 + - - -
135C THR* 3.8 31.2 - - + +
138C ILE* 3.8 11.7 - - + -
139C PRO* 3.9 22.7 - - + -
170C ILE* 3.3 27.8 - - + -
172C GLU* 5.8 0.7 - - - -
175C VAL* 4.2 16.4 - - + -
177C ILE* 4.4 15.7 - - + +
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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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6C GLY 2.9 19.2 + - - +
7C GLY 3.5 7.4 - - - +
8C GLU 3.2 0.2 - - - -
9C LEU* 1.3 75.5 - - - +
11C VAL* 1.3 59.3 + - - +
13C THR* 3.2 2.8 + - - -
14C LEU* 2.9 41.3 + - + +
33C ILE* 4.1 13.9 - - + -
98C LEU* 4.0 27.6 - - + -
138C ILE* 3.6 19.7 - - + +
142C VAL* 4.6 12.4 - - + +
161C LEU* 4.0 13.2 - - + -
166C LEU* 3.9 21.3 - - + -
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Residues in contact with VAL 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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7C GLY 3.1 7.0 + - - +
8C GLU 3.1 2.7 + - - +
10C VAL* 1.3 76.8 - - + +
12C ARG* 1.3 57.8 + - - +
14C LEU* 3.2 10.9 + - + +
15C ILE* 2.8 51.3 + - + +
33C ILE* 3.6 25.8 - - + +
36C ALA* 3.5 39.5 - - + +
37C CYS* 3.7 18.8 - - - -
40C HIS* 4.2 13.0 - - + +
42C VAL* 4.8 2.7 - - + -
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Residues in contact with ARG 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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4C ILE* 3.9 25.2 - - - +
8C GLU* 2.5 50.4 + - - +
9C LEU* 4.0 4.5 - - - +
11C VAL* 1.3 71.1 - - - +
13C THR* 1.3 61.3 + - - +
15C ILE* 3.4 9.7 + - + +
16C LYS* 3.2 24.6 + - - +
40C HIS* 4.3 19.1 + - + +
172C GLU* 2.9 39.6 + - - +
177C ILE* 4.2 26.8 - - + +
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Residues in contact with THR 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 LEU 2.9 18.1 + - - -
10C VAL 3.7 3.8 - - - -
12C ARG* 1.3 72.3 - - - +
14C LEU* 1.3 65.3 + - - +
16C LYS* 3.2 2.8 + - - +
17C ALA* 3.0 22.4 + - - +
139C PRO* 3.3 44.6 - - + +
142C VAL* 3.8 20.2 - - + -
143C MSE 4.0 19.9 - - + +
177C ILE* 3.8 17.8 - - + +
178C PRO* 5.0 2.2 - - + +
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Residues in contact with LEU 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 VAL* 2.9 32.6 + - + +
11C VAL* 3.2 15.5 + - + +
13C THR* 1.3 76.8 - - - +
15C ILE* 1.3 62.1 + - + +
17C ALA* 3.2 3.3 + - - +
18C GLY 3.2 4.7 + - - -
19C VAL* 3.0 46.5 + - + +
22C LEU* 4.0 36.1 - - + -
69C VAL* 4.4 3.4 - - + -
96C LEU* 3.9 20.4 - - + -
98C LEU* 4.2 7.2 - - + -
142C VAL* 3.9 21.3 - - + -
146C ILE* 4.2 6.7 - - + -
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Residues in contact with ILE 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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11C VAL* 2.8 36.0 + - + +
12C ARG* 3.5 11.0 - - + +
13C THR 3.2 0.2 - - - -
14C LEU* 1.3 75.9 - - + +
16C LYS* 1.3 58.7 + - + +
18C GLY* 2.8 21.5 + - - -
19C VAL 4.5 8.9 - - - +
40C HIS* 3.9 25.6 - - + +
42C VAL* 3.4 33.0 - - + -
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Residues in contact with LYS 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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12C ARG 3.2 10.6 + - - +
13C THR 3.2 8.5 + - - +
15C ILE* 1.3 82.2 - - + +
17C ALA* 1.3 59.3 + - - +
18C GLY* 3.1 1.5 + - - -
143C MSE 5.7 0.4 - - - -
176C ILE* 6.0 0.4 - - - +
177C ILE* 2.8 35.7 + - + +
178C PRO 3.4 23.7 - - - +
179C ASP* 3.6 27.8 + - - +
180C LEU* 4.6 10.5 + - - +
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Residues in contact with ALA 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 THR 3.0 12.6 + - - +
14C LEU 3.5 9.4 - - - +
15C ILE 3.2 0.4 - - - -
16C LYS* 1.3 74.7 - - - +
18C GLY* 1.3 59.2 + - - +
19C VAL* 4.2 7.1 - - + +
67C LEU* 5.5 0.4 - - + -
143C MSE 3.7 26.9 - - + -
146C ILE* 3.8 17.3 - - + -
180C LEU* 4.1 24.4 - - + +
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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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15C ILE 2.8 15.5 + - - -
16C LYS 3.1 1.7 - - - -
17C ALA* 1.3 79.3 - - - +
19C VAL* 1.3 66.1 + - - +
20C GLU* 3.6 15.6 + - - +
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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