Contacts of the helix formed by residues 3 - 15 (chain C) in PDB entry 6S1M
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 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ALA* 1.3 77.5 - - + +
4C GLN* 1.3 70.1 + - + +
5C LEU 3.3 0.3 + - - -
6C TYR* 3.3 33.4 + - + -
7C LEU* 2.9 32.4 + - - +
43C ASP* 3.9 4.5 - - - +
47C ARG* 2.7 45.0 + - - -
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Residues in contact with GLN 4 (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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2C ALA 3.4 3.2 - - - +
3C ASP* 1.3 90.1 - - - +
5C LEU* 1.3 57.4 + - - +
7C LEU* 3.9 24.4 - - - +
8C GLU* 2.9 42.8 + - + +
47C ARG* 4.7 5.2 + - - -
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Residues in contact with LEU 5 (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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2C ALA* 3.4 24.3 + - - +
3C ASP 3.2 0.4 - - - -
4C GLN* 1.3 78.0 - - - +
6C TYR* 1.3 60.2 + - + +
8C GLU* 3.9 2.4 - - - +
9C ASN* 3.0 42.6 + - - +
30C LEU* 6.4 1.3 - - + -
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Residues in contact with TYR 6 (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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17B PRO* 3.7 16.4 - - + +
2C ALA 3.5 16.8 - - - -
3C ASP* 3.3 33.5 + - + +
5C LEU* 1.3 79.3 - - + +
7C LEU* 1.3 66.0 + - + +
9C ASN* 4.0 8.7 - - - +
10C ILE* 2.9 41.8 + - + +
30C LEU* 4.3 12.6 - - + -
40C MET* 4.0 59.0 - - + -
43C ASP* 2.3 35.4 + - + +
44C TYR* 5.1 4.0 - - + -
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Residues in contact with LEU 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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3C ASP* 2.9 24.5 + - - +
4C GLN* 3.9 20.6 - - - +
6C TYR* 1.3 85.2 - - + +
8C GLU* 1.3 80.4 + - - +
10C ILE* 3.5 3.9 + - - +
11C ASP* 3.0 29.8 + - + +
43C ASP* 6.3 0.4 - - - -
44C TYR* 4.4 20.9 - - + -
47C ARG* 3.8 41.3 - - + +
48C LYS* 4.6 19.3 - - - +
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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 GLN* 2.9 30.0 + - + +
5C LEU* 4.0 2.5 - - - +
7C LEU* 1.3 96.8 - - + +
9C ASN* 1.3 60.6 + - - +
11C ASP* 3.3 14.4 + - - +
12C GLU* 2.9 31.3 + - - +
48C LYS* 5.8 0.5 + - - -
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Residues in contact with ASN 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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5C LEU* 3.0 34.1 + - - +
6C TYR* 3.7 7.0 - - - +
7C LEU 3.4 0.2 - - - -
8C GLU* 1.3 76.7 - - - +
10C ILE* 1.3 57.7 + - + +
12C GLU* 3.0 23.8 - - - +
13C PHE* 2.9 40.3 + - + -
26C LEU* 6.1 0.2 - - + -
30C LEU* 3.5 34.2 - - + +
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Residues in contact with ILE 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 TYR* 2.9 35.6 + - + +
7C LEU 4.0 2.9 - - - +
9C ASN* 1.3 76.8 - - + +
11C ASP* 1.3 56.7 + - - +
13C PHE* 4.3 5.4 - - - -
14C VAL* 2.9 42.6 + - + +
21C VAL* 5.8 1.3 - - + -
26C LEU* 3.8 41.3 - - + -
30C LEU* 5.8 0.4 - - + -
40C MET* 4.5 7.6 - - + +
41C LEU* 5.0 4.7 - - + -
44C TYR* 3.6 49.4 - - + -
103C ILE* 4.6 4.3 - - + -
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Residues in contact with ASP 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 LEU* 3.0 19.2 + - + +
8C GLU* 3.3 18.7 + - - +
10C ILE* 1.3 76.7 - - - +
12C GLU* 1.3 60.0 + - - +
14C VAL 4.3 0.2 - - - -
15C THR* 2.9 39.9 + - - +
16C ASP* 4.1 1.0 + - - +
44C TYR* 3.5 22.2 + - + -
48C LYS* 3.8 21.9 + - - +
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Residues in contact with GLU 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 GLU 2.9 21.0 + - - +
9C ASN* 3.0 26.4 - - - +
11C ASP* 1.3 77.1 - - - +
13C PHE* 1.3 89.0 + - - +
14C VAL 3.4 0.6 + - - -
16C ASP* 3.4 15.9 - - + +
17C GLN* 3.2 48.7 + - - +
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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 ASN* 2.9 36.1 + - + +
10C ILE* 3.8 5.4 - - - +
12C GLU* 1.3 101.9 - - - +
14C VAL* 1.3 61.8 + - - +
17C GLN* 3.9 19.6 - - - +
18C ASN 4.0 2.8 + - - -
19C LYS* 3.6 27.3 + - + +
21C VAL* 4.5 7.4 - - + +
25C TRP* 3.7 39.7 - + + -
26C LEU* 4.5 14.6 - - + -
29C THR* 3.8 31.2 - - + -
30C LEU* 5.3 0.9 - - + -
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Residues in contact with VAL 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 ILE* 2.9 27.0 + - + +
13C PHE* 1.3 77.9 - - + +
15C THR* 1.3 75.9 + - + +
16C ASP 3.5 0.2 - - - -
18C ASN* 3.5 20.8 - - - -
19C LYS 3.9 8.8 + - - +
21C VAL* 3.8 20.6 - - + -
44C TYR* 4.7 3.8 - - + +
57C LEU* 4.6 19.5 - - + -
103C ILE* 3.7 27.4 - - + +
104C GLN* 4.8 7.4 - - - +
105C LYS* 3.5 20.5 - - + +
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Residues in contact with THR 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 ASP* 2.9 39.3 + - - +
14C VAL* 1.3 92.6 - - + +
16C ASP* 1.3 60.8 + - - +
18C ASN* 3.3 11.8 - - - +
44C TYR* 4.1 7.6 - - - +
57C LEU* 6.2 0.7 - - + -
105C LYS* 4.4 21.0 + - + -
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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