Contacts of the helix formed by residues 2 - 12 (chain A) in PDB entry 4W56
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 ASN 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 76.6 - - - +
3A ILE* 1.3 66.4 + - + +
4A PHE* 2.9 27.9 + - + +
5A GLU* 3.0 31.3 + - - +
6A MET* 3.0 23.2 + - - +
97A CYS* 4.8 2.0 - - - -
158A TRP* 4.3 11.4 - - - -
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Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 1.3 75.9 - - + +
4A PHE* 1.3 80.9 + - + +
6A MET* 4.0 14.1 - - - -
7A LEU* 3.0 48.4 + - + +
71A VAL* 4.2 12.1 - - + -
97A CYS* 3.4 46.5 - - - +
100A ILE* 3.8 31.2 - - + -
101A ASN 4.1 1.8 - - - +
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Residues in contact with PHE 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 2.9 12.4 + - - +
3A ILE* 1.3 92.0 - - + +
5A GLU* 1.3 62.0 + - + +
8A ARG* 2.9 31.1 + - - +
67A PHE* 3.5 30.7 - + + -
68A ASN* 3.1 33.7 - - - -
71A VAL* 3.7 33.2 - - + -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.1 42.6 + - + +
2A ASN* 3.0 29.2 + - - +
4A PHE* 1.3 77.2 - - + +
6A MET* 1.3 63.5 + - - +
8A ARG* 3.4 5.5 + - - +
9A ILE* 3.0 30.2 + - + +
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Residues in contact with MET 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.6 6.7 - - - -
2A ASN 3.0 16.6 + - - +
3A ILE* 3.7 7.2 - - - +
5A GLU* 1.3 77.4 - - - +
7A LEU* 1.3 57.4 + - - +
9A ILE* 3.2 5.9 + - - +
10A ASP* 3.0 26.7 + - - -
97A CYS* 3.8 21.3 - - - +
98A ALA* 3.9 23.3 - - + +
101A ASN* 3.4 20.0 - - + +
149A VAL* 4.6 3.4 - - + -
152A THR* 4.1 10.3 - - + +
158A TRP* 3.7 26.0 - - + -
161A TYR* 3.5 46.6 - - + +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.0 40.0 + - + +
6A MET* 1.3 74.9 - - - +
8A ARG* 1.3 56.0 + - - +
10A ASP* 4.3 2.0 - - + +
11A GLU* 2.7 42.7 + - + +
29A ILE* 4.5 0.2 - - - -
67A PHE* 3.6 16.6 - - + -
71A VAL* 4.1 11.0 - - + -
100A ILE* 4.6 2.5 - - + -
101A ASN* 3.7 20.0 - - - +
104A PHE* 3.6 46.4 - - + -
145A ARG* 3.3 30.1 - - - +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE 2.9 19.5 + - - +
5A GLU* 3.7 7.4 - - - +
7A LEU* 1.3 76.7 - - - +
9A ILE* 1.3 61.4 + - + +
12A GLY* 3.0 48.4 + - - -
13A LEU* 3.6 33.7 + - - +
29A ILE* 4.1 22.4 - - - +
60A LYS* 6.2 0.6 - - - +
67A PHE* 3.9 6.8 - - + -
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.2 15.7 - - + -
5A GLU* 3.0 20.8 + - + +
6A MET 3.4 6.1 - - - +
7A LEU 3.2 0.2 - - - -
8A ARG* 1.3 82.4 + - + +
10A ASP* 1.3 67.7 + - - +
11A GLU 3.5 0.2 + - - -
12A GLY* 3.9 4.0 + - - -
148A ARG* 4.6 7.4 + - - +
161A TYR* 4.0 29.6 - - + +
164A LEU* 3.8 53.4 - - + +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET 3.0 13.5 + - - +
7A LEU* 3.9 3.8 - - - +
9A ILE* 1.3 77.4 - - - +
11A GLU* 1.3 59.7 + - - +
101A ASN* 2.8 19.4 + - - -
145A ARG* 3.7 41.8 + - - +
148A ARG* 2.8 44.0 + - - +
161A TYR* 2.6 27.7 + - - -
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 2.7 29.5 + - + +
10A ASP* 1.3 75.9 - - - +
12A GLY* 1.3 61.9 + - - +
14A ARG* 5.9 1.2 - - - +
18A TYR* 4.1 16.6 + - - -
29A ILE* 3.7 15.7 - - + +
30A GLY* 3.6 20.0 - - - +
104A PHE* 3.5 33.1 - - + -
105A GLN* 4.6 4.5 - - - +
145A ARG* 2.9 34.1 + - - -
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Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.0 28.4 + - - -
9A ILE 3.9 2.9 + - - -
10A ASP 3.6 1.2 - - - -
11A GLU* 1.3 82.9 - - - +
13A LEU* 1.3 61.2 + - - +
14A ARG* 5.4 1.6 - - - -
28A GLY 4.3 0.7 - - - -
29A ILE* 3.4 24.6 - - - +
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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