Contacts of the helix formed by residues 7 - 20 (chain C) in PDB entry 2P6T
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 ASP 7 (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 3.8 7.9 + - - +
6C LEU* 1.3 79.8 - - - +
8C LYS* 1.3 64.9 + - - +
9C THR* 3.2 12.8 + - - -
10C ASP* 3.3 19.6 + - - +
11C ILE* 3.5 12.4 + - - +
42C ARG* 3.3 28.0 + - - -
157C LEU 6.0 0.2 - - - -
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Residues in contact with LYS 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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7C ASP* 1.3 75.5 - - - +
9C THR* 1.3 69.0 + - - +
11C ILE* 3.3 12.1 + - - +
12C LYS* 3.4 14.1 + - + +
158C LEU* 3.8 29.4 - - + +
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Residues in contact with THR 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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7C ASP* 3.3 3.4 + - - -
8C LYS* 1.3 82.6 + - - +
10C ASP* 1.3 66.6 + - - +
12C LYS* 2.9 18.4 + - + +
13C ILE* 3.0 11.2 + - + +
32C VAL* 4.2 21.8 - - + +
33C ALA 5.2 0.9 - - - +
34C LEU* 4.0 25.1 - - + -
42C ARG* 3.3 32.9 + - - +
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Residues in contact with ASP 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 4.9 2.1 + - - -
6C LEU* 3.5 34.0 + - + -
7C ASP* 3.3 16.6 + - - +
9C THR* 1.3 77.8 - - - +
11C ILE* 1.3 59.6 + - - +
13C ILE* 3.3 12.2 - - - +
14C LEU* 3.2 27.7 + - - +
42C ARG* 2.9 41.9 + - - +
46C LEU* 3.6 21.5 - - + +
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Residues in contact with ILE 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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6C LEU* 4.7 13.7 - - + +
7C ASP 3.5 17.9 - - - +
8C LYS* 3.6 5.4 - - - +
9C THR 3.0 0.6 - - - -
10C ASP* 1.3 73.9 - - - +
12C LYS* 1.3 61.2 + - - +
13C ILE 3.1 1.8 - - - -
14C LEU* 3.1 8.9 + - + +
15C GLN* 2.8 43.4 + - + +
154C LEU* 3.7 33.2 - - + +
157C LEU* 3.4 37.5 - - + +
158C LEU* 3.3 34.8 - - + -
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Residues in contact with LYS 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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8C LYS* 3.4 12.1 + - + +
9C THR* 2.9 13.0 + - + +
11C ILE* 1.3 77.6 - - - +
13C ILE* 1.3 60.2 + - - +
15C GLN* 4.0 21.0 + - + +
16C VAL* 3.2 35.7 + - + +
31C ARG* 3.5 26.9 - - - +
32C VAL* 4.0 16.3 - - + +
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Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.0 13.0 + - + +
10C ASP* 3.3 23.1 - - - +
11C ILE 3.1 0.2 - - - -
12C LYS* 1.3 76.1 - - - +
14C LEU* 1.3 59.5 + - + +
16C VAL* 3.4 3.5 + - - +
17C LEU* 2.9 49.8 + - + +
28C LEU* 4.2 13.0 - - + -
32C VAL* 4.2 21.3 - - + -
34C LEU* 4.8 3.1 - - + -
39C CYS* 4.8 6.5 - - - +
42C ARG* 3.5 38.8 - - + -
43C LEU* 4.1 11.2 - - + +
46C LEU* 4.1 13.2 - - + -
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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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6C LEU* 4.5 13.5 - - + -
10C ASP 3.2 13.9 + - - +
11C ILE* 3.1 12.4 + - + +
13C ILE* 1.3 77.4 - - + +
15C GLN* 1.3 60.1 + - - +
17C LEU* 4.5 4.7 - - + +
18C GLN* 2.9 35.7 + - - +
43C LEU* 6.5 0.2 - - + -
46C LEU* 4.0 16.8 - - + -
51C ILE* 3.3 25.1 - - + -
52C VAL* 3.6 12.1 - - + -
154C LEU* 3.8 10.8 - - + -
157C LEU* 6.0 0.9 - - + -
59D LEU* 3.2 43.7 - - + -
64D VAL* 4.5 9.4 - - + -
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Residues in contact with GLN 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 ILE* 2.8 30.2 + - - +
12C LYS* 4.0 27.3 + - + +
14C LEU* 1.3 74.1 - - - +
16C VAL* 1.3 64.2 + - + +
18C GLN* 3.7 8.8 + - - +
19C GLU* 3.1 24.0 - - - +
154C LEU* 3.9 29.9 - - + +
155C ASN* 4.5 19.4 + - - +
158C LEU* 5.3 7.2 - - - +
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Residues in contact with VAL 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 LYS* 3.2 35.8 + - + +
13C ILE 3.8 2.9 - - - +
14C LEU 3.3 0.2 - - - -
15C GLN* 1.3 78.0 - - + +
17C LEU* 1.3 56.6 + - - +
19C GLU* 3.3 5.4 + - - +
20C ASN* 3.0 29.9 + - - +
23C LEU* 3.4 32.3 - - + -
28C LEU* 3.4 11.9 - - + -
31C ARG* 3.6 36.8 - - + +
32C VAL* 5.0 0.2 - - + -
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Residues in contact with LEU 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 ILE* 2.9 26.1 + - + +
14C LEU* 4.1 6.1 - - + +
16C VAL* 1.3 72.0 - - - +
18C GLN* 1.3 65.2 + - - +
19C GLU 3.1 2.2 - - - -
20C ASN 4.1 5.8 - - - +
21C GLY 3.1 25.3 + - - +
23C LEU* 4.0 18.6 - - + -
28C LEU* 3.3 28.7 - - + -
43C LEU* 3.5 39.3 - - + -
52C VAL* 5.2 4.7 - - + -
55C TYR* 3.6 14.4 - - + +
22D ARG* 4.8 7.0 - - - +
57D ALA* 3.1 22.7 + - + +
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Residues in contact with GLN 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 LEU 2.9 17.2 + - - +
15C GLN* 4.0 7.4 + - - +
16C VAL 3.4 0.2 - - - -
17C LEU* 1.3 77.1 - - - +
19C GLU* 1.3 56.4 + - - +
150C THR* 4.5 2.5 + - - +
151C SER* 3.3 26.2 + - - +
152C LEU* 3.0 55.3 + - - +
154C LEU* 4.2 8.3 - - - +
54D GLN* 4.6 1.0 - - - +
56D ALA* 3.0 25.3 - - - +
57D ALA* 3.1 23.9 - - + +
59D LEU* 2.9 34.2 + - + +
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Residues in contact with GLU 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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15C GLN 3.1 20.2 - - - +
16C VAL* 3.3 1.8 + - - +
17C LEU 3.1 0.4 - - - -
18C GLN* 1.3 79.6 - - - +
20C ASN* 1.3 74.2 + - - +
21C GLY 3.6 0.9 - - - -
149C THR* 4.7 3.3 + - - -
151C SER* 3.0 28.0 + - - +
54D GLN* 3.6 19.9 - - - +
55D TYR 3.3 10.6 - - - +
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Residues in contact with ASN 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 VAL* 3.0 17.1 + - - +
17C LEU* 3.4 6.9 - - - +
19C GLU* 1.3 88.7 - - - +
21C GLY* 1.3 56.0 + - - +
22C ARG 3.0 6.3 - - - -
23C LEU* 2.8 44.3 + - + +
31C ARG* 3.5 26.5 + - - +
55D TYR 3.5 2.2 - - - -
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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