Contacts of the helix formed by residues 3 - 16 (chain C) in PDB entry 3KXC
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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19A PHE* 5.5 0.5 - - - +
62A ARG* 2.6 46.5 + - - -
85A MET 3.3 24.0 + - - +
86A TYR* 2.8 20.2 + - + +
2C ALA* 1.3 74.3 - - - +
4C GLU* 1.3 66.3 + - - +
5C ALA* 3.0 22.7 + - - +
6C LEU* 3.3 18.0 + - - +
7C PHE* 4.3 1.6 + - - +
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Residues in contact with GLU 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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18A LEU* 6.4 1.6 - - + -
2C ALA 3.6 2.5 + - - -
3C ASP* 1.3 75.2 + - - +
5C ALA* 1.3 65.7 + - - +
6C LEU 3.0 1.2 + - - -
7C PHE* 3.1 19.3 + - + +
8C LEU* 3.2 28.0 + - + +
76C VAL 3.9 10.0 - - - +
77C PHE* 5.8 0.3 - - - -
78C LYS* 3.6 34.1 - - - +
100C ARG* 2.5 48.4 + - - -
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Residues in contact with ALA 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.7 4.0 - - + -
58A ASP* 3.9 17.5 - - - +
62A ARG* 3.6 13.2 - - - +
86A TYR* 4.1 8.1 - - + -
3C ASP* 3.0 16.9 + - - +
4C GLU* 1.3 77.4 - - - +
6C LEU* 1.3 55.4 + - - +
8C LEU* 3.4 11.9 + - - +
9C LEU* 3.0 38.5 + - + +
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Residues in contact with LEU 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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19A PHE* 3.7 20.8 - - + -
51A ILE* 5.4 8.1 - - + +
55A LEU* 4.1 19.7 - - + -
86A TYR* 3.4 38.8 - - + +
87A LEU* 3.5 21.3 - - + -
181A PLM 3.4 36.6 - - + -
2C ALA* 4.2 7.9 - - + -
3C ASP 3.3 9.1 + - - +
4C GLU 3.0 1.0 + - - -
5C ALA* 1.3 74.1 - - - +
7C PHE* 1.3 61.1 + - - +
9C LEU* 3.6 3.9 + - - +
10C LEU* 3.0 30.7 + - - +
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Residues in contact with PHE 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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16A SER* 5.8 0.4 - - - +
18A LEU* 3.7 39.7 - - + -
19A PHE* 3.9 16.6 - - + +
22A THR* 3.4 37.9 - - + -
3C ASP 4.3 1.0 + - - +
4C GLU* 3.1 14.5 + - + +
6C LEU* 1.3 78.8 - - - +
8C LEU* 1.3 71.6 + - + +
10C LEU* 3.3 1.2 + - - +
11C HIS* 2.8 38.5 + - + +
76C VAL* 4.6 12.1 - - + -
77C PHE* 4.7 2.2 - + - -
101C LEU* 4.0 26.5 - - + -
121C PHE* 3.7 28.3 - + - -
125C LEU* 5.1 0.7 - - + -
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Residues in contact with LEU 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 GLU* 3.2 37.6 + - + +
5C ALA* 3.7 10.5 - - - +
6C LEU 3.3 0.2 - - - -
7C PHE* 1.3 87.3 - - + +
9C LEU* 1.3 64.5 + - + +
11C HIS* 3.7 4.2 + - - +
12C ASN* 3.2 23.7 + - - +
77C PHE* 6.0 2.5 - - + -
100C ARG* 4.2 25.8 - - + +
101C LEU* 3.6 27.1 - - + +
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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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51A ILE* 3.9 24.2 - - + +
54A ARG* 4.1 33.4 - - + +
55A LEU* 3.7 47.8 - - + +
58A ASP* 5.5 2.9 - - + -
5C ALA* 3.0 21.6 + - + +
6C LEU* 4.0 3.6 - - - +
8C LEU* 1.3 78.8 - - + +
10C LEU* 1.3 59.4 + - - +
12C ASN* 3.4 6.5 + - + +
13C GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 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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19A PHE* 3.7 27.8 - - + -
22A THR* 3.5 30.7 - - + +
23A TYR* 4.0 20.0 - - + +
26A LEU* 4.2 15.7 - - + -
47A MET* 4.5 4.7 - - + -
51A ILE* 3.8 22.8 - - + +
130A LEU* 4.7 4.3 - - + -
6C LEU 3.0 19.4 + - - +
7C PHE* 3.7 3.8 - - - +
9C LEU* 1.3 72.3 - - - +
11C HIS* 1.3 61.5 + - - +
13C GLU* 3.2 1.6 + - - +
14C MET* 2.8 46.5 + - + +
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Residues in contact with HIS 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 PHE* 2.8 31.3 + - + +
8C LEU 4.0 3.6 - - - +
10C LEU* 1.3 72.8 - - - +
12C ASN* 1.3 66.4 + - + +
14C MET* 3.3 16.8 + - + +
15C VAL* 3.0 44.3 + - + +
36C LEU* 5.6 0.6 - - + +
101C LEU* 3.6 39.6 - - + +
118C TYR* 3.4 30.4 + + - -
121C PHE* 3.5 42.2 - - + +
122C THR* 5.0 0.2 - - - -
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Residues in contact with ASN 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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54A ARG* 4.3 27.3 - - - +
8C LEU 3.2 18.6 + - - +
9C LEU* 3.7 9.0 - - + +
10C LEU 3.2 0.2 - - - -
11C HIS* 1.3 79.2 - - + +
13C GLU* 1.3 63.4 + - - +
15C VAL* 3.1 20.4 - - - +
16C SER* 3.2 17.1 + - - -
101C LEU 5.4 0.9 - - - +
118C TYR* 3.4 26.5 + - - -
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Residues in contact with GLU 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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46A LYS* 4.0 9.2 + - - -
47A MET* 3.7 38.9 - - + +
50A ASN* 2.9 46.1 + - - +
51A ILE* 3.8 12.1 - - + +
9C LEU 2.9 17.9 + - - +
10C LEU 3.6 4.0 - - - +
12C ASN* 1.3 78.2 + - - +
14C MET* 1.3 58.1 + - - +
16C SER* 2.9 36.2 + - - +
17C GLY 3.3 6.6 - - - +
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Residues in contact with MET 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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22A THR* 3.5 29.2 - - + -
26A LEU* 3.9 24.0 - - + -
47A MET* 3.8 16.4 - - + -
10C LEU* 2.8 30.5 + - + +
11C HIS* 3.3 33.6 + - + +
13C GLU* 1.3 73.3 - - - +
15C VAL* 1.3 62.4 + - - +
17C GLY 3.4 16.4 - - - -
32C CYS* 5.3 3.8 - - - -
36C LEU* 4.2 18.6 - - + +
39C MET* 4.3 21.5 - - + +
121C PHE* 4.7 10.3 - - + -
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Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C HIS* 3.0 39.0 + - + +
12C ASN* 3.1 17.3 - - - +
14C MET* 1.3 77.2 - - - +
16C SER* 1.3 57.2 + - - +
17C GLY 3.3 5.4 + - - -
32C CYS* 5.1 4.0 - - - -
36C LEU* 4.0 18.6 - - + +
117C LYS* 3.7 51.8 + - + +
118C TYR* 3.2 41.1 - - + +
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Residues in contact with SER 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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46A LYS* 5.2 1.0 + - - -
12C ASN* 3.2 22.2 + - - -
13C GLU* 2.9 27.2 + - - +
15C VAL* 1.3 75.3 - - - +
17C GLY* 1.3 58.8 + - - +
117C LYS* 5.6 1.6 - - - +
118C TYR* 5.0 7.6 - - - -
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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