Contacts of the strand formed by residues 7 - 15 (chain C) in PDB entry 3LAW
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 VAL 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 LYS 4.2 6.1 - - - +
6C LYS* 1.3 82.4 - - - +
8C LEU* 1.3 56.6 + - - +
9C LEU* 3.6 10.0 + - + -
55C ARG* 5.0 14.6 - - + +
56C LEU 3.3 13.1 + - - +
57C VAL* 3.6 8.5 - - + +
58C THR 2.7 29.3 + - - -
174C LEU* 3.9 26.0 - - + -
177C GLU* 3.6 17.3 - - - +
129E PHE* 3.8 2.9 - - - -
130E GLU* 5.3 8.7 - - + +
131E ASN* 2.7 26.7 - - - +
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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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7C VAL* 1.3 69.5 - - - +
9C LEU* 1.3 67.5 + - - +
10C LYS* 4.3 1.1 + - + -
47C THR* 5.6 1.1 - - + -
58C THR* 3.5 23.6 - - + +
60C GLN* 4.5 28.0 - - + +
82C ASP* 4.5 1.7 - - - +
177C GLU* 4.7 1.0 - - - +
89E ASP* 5.0 0.4 - - - +
91E THR* 3.5 27.1 - - + +
126E LYS* 4.9 11.0 - - - +
129E PHE* 3.3 48.3 - - + -
131E ASN* 2.9 30.9 + - - +
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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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7C VAL* 4.0 12.6 - - + +
8C LEU* 1.3 83.8 - - - +
10C LYS* 1.3 60.3 + - - +
11C VAL* 3.8 5.0 + - + +
57C VAL* 3.3 31.0 - - + -
58C THR 2.9 8.8 + - - +
59C MET* 3.8 4.8 - - + -
60C GLN* 3.0 29.9 + - - +
82C ASP* 3.4 5.8 - - - +
170C ALA 3.7 22.4 - - - +
173C ALA* 4.0 16.2 - - + +
174C LEU* 3.8 18.2 - - + +
177C GLU* 3.6 33.0 - - + -
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Residues in contact with LYS 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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8C LEU* 4.3 1.0 + - + +
9C LEU* 1.3 71.9 - - - +
11C VAL* 1.3 63.3 - - - +
12C ILE* 5.2 2.5 - - + +
60C GLN* 3.8 14.1 - - - +
62C TRP* 3.6 37.5 - - + +
76C ALA 4.9 0.2 + - - -
77C PHE* 2.7 42.6 + - + +
79C ARG 3.2 16.6 + - - +
80C GLY* 3.9 8.7 - - - +
81C ALA* 3.5 20.9 - - + +
82C ASP* 2.6 40.2 + - - +
83C CYS 3.5 3.1 + - - -
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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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9C LEU 4.4 3.8 - - - +
10C LYS* 1.3 81.6 - - - +
12C ILE* 1.3 56.2 + - - +
59C MET* 3.5 33.9 - - + -
60C GLN 2.9 12.3 + - - +
61C ILE* 3.3 13.1 - - + +
62C TRP* 2.8 33.3 + - - -
83C CYS* 3.6 9.6 - - + +
85C VAL* 3.8 16.6 - - + -
166C PHE* 5.2 2.0 - - + -
169C ILE* 3.6 24.7 - - + -
173C ALA* 4.2 20.4 - - + -
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Residues in contact with ILE 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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10C LYS* 4.3 2.2 - - + -
11C VAL* 1.3 74.0 - - - +
13C ILE* 1.3 66.3 + - - +
14C LEU* 3.8 27.6 - - + -
62C TRP* 3.9 11.0 - - + +
64C THR* 4.1 13.0 - - + -
77C PHE* 3.7 28.9 - - + -
78C TYR* 4.1 19.1 - - + +
81C ALA* 4.2 10.1 - - + -
83C CYS 3.1 10.4 + - - +
84C CYS* 3.5 4.6 - - - -
85C VAL* 2.8 27.1 + - - +
106C PHE* 3.7 29.6 - - + -
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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
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11C VAL* 5.0 0.4 - - + -
12C ILE* 1.3 76.7 - - - +
14C LEU* 1.3 56.1 + - - +
21C LYS* 3.7 27.2 - - + +
24C LEU* 5.6 2.7 - - + -
25C MET* 4.6 14.6 - - + +
61C ILE* 3.4 31.2 - - + -
62C TRP 3.2 10.2 + - - +
63C ASP* 5.2 4.0 - - - +
64C THR* 2.7 32.7 + - - +
85C VAL* 3.4 23.1 - - + +
87C VAL* 3.6 28.5 - - + -
166C PHE* 4.2 20.9 - - + -
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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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12C ILE* 3.8 18.6 - - + -
13C ILE* 1.3 75.2 - - - +
15C GLY* 1.3 59.6 + - - +
21C LYS* 3.6 5.1 - - - +
64C THR* 4.1 14.6 - - + +
78C TYR* 3.4 25.8 - - - +
84C CYS* 3.6 25.4 - - - -
85C VAL 2.6 13.4 + - - +
86C LEU* 3.3 12.9 - - + +
87C VAL* 2.9 25.8 + - - +
102C TRP* 3.9 36.3 - - + +
105C GLU* 5.8 0.4 - - + -
106C PHE* 3.8 23.3 - - + +
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Residues in contact with GLY 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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14C LEU* 1.3 77.3 - - - +
16C ASP* 1.3 69.2 + - - -
17C SER 3.7 0.2 + - - -
19C VAL* 4.2 0.7 - - - -
21C LYS* 2.9 21.1 + - - +
64C THR* 5.0 0.4 + - - -
65C ALA 5.3 0.2 - - - -
66C GLY* 3.8 5.0 - - - -
87C VAL 3.6 13.9 - - - -
99C LEU* 5.7 0.7 - - - -
102C TRP* 3.7 29.8 - - - -
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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