Contacts of the helix formed by residues 4 - 14 (chain W) in PDB entry 2EIN
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 ARG 4 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224P LYS 5.0 2.2 + - - -
2W GLU* 3.2 48.1 + - - +
3W ASN* 1.3 78.6 - - - +
5W VAL* 1.3 66.6 + - - +
6W ALA* 3.2 3.1 - - - -
7W GLU* 3.0 54.5 + - - +
8W LYS* 3.3 16.4 + - + +
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Residues in contact with VAL 5 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P THR* 3.9 16.4 - - + +
67P PHE* 4.3 4.5 - - + -
224P LYS 3.4 22.4 - - - +
225P PHE 3.7 16.6 - - - +
226P HIS* 4.3 8.5 - - + +
12S GLN* 3.7 24.9 - - + +
3W ASN* 3.1 20.2 + - - +
4W ARG* 1.3 78.1 - - - +
6W ALA* 1.3 51.4 + - - +
8W LYS* 3.0 10.5 + - - +
9W GLN* 2.8 54.5 + - + +
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Residues in contact with ALA 6 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W ASN* 4.7 1.9 + - - +
4W ARG 3.2 0.8 - - - -
5W VAL* 1.3 75.8 - - - +
7W GLU* 1.3 66.9 + - + +
9W GLN* 3.4 17.5 + - - +
10W LYS* 3.1 24.4 + - - +
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Residues in contact with GLU 7 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ARG* 3.0 55.6 + - + +
6W ALA* 1.3 78.2 - - + +
8W LYS* 1.3 64.2 + - + +
10W LYS* 3.4 9.6 + - - +
11W LEU* 3.0 27.0 + - - +
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Residues in contact with LYS 8 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P PHE* 3.2 36.7 - - + +
1270P CDL 2.9 62.4 + - - +
4W ARG* 3.8 13.5 - - + +
5W VAL* 3.0 5.2 + - - +
7W GLU* 1.3 83.2 - - + +
9W GLN* 1.3 58.1 + - - +
11W LEU* 4.2 19.9 - - + +
12W PHE* 2.9 46.7 + - + +
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Residues in contact with GLN 9 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P THR 3.3 8.5 + - - +
67P PHE* 3.4 26.9 - - - +
12S GLN* 3.0 20.4 + - - +
14S THR* 2.9 38.5 - - - +
5W VAL* 2.8 29.7 + - + +
6W ALA* 3.4 23.0 + - - +
7W GLU 3.3 0.2 - - - -
8W LYS* 1.3 72.6 - - - +
10W LYS* 1.3 57.9 + - - +
12W PHE 3.8 0.5 - - - -
13W GLN* 3.0 42.9 + - - +
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Residues in contact with LYS 10 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W ALA 3.1 13.2 + - - +
7W GLU* 3.4 13.2 - - - +
9W GLN* 1.3 74.4 - - - +
11W LEU* 1.3 66.8 + - - +
13W GLN* 3.0 5.5 + - - +
14W GLU* 2.8 30.8 + - + +
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Residues in contact with LEU 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7W GLU 3.0 16.0 + - - +
8W LYS* 3.8 20.2 - - + +
9W GLN 3.4 0.2 - - - -
10W LYS* 1.3 74.7 - - - +
12W PHE* 1.3 87.0 + - + +
14W GLU* 3.2 35.8 - - - +
16W ASN* 5.4 0.5 + - - -
23W LYS* 4.0 22.3 - - - +
24W GLY 4.5 13.7 - - - +
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Residues in contact with PHE 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P ARG* 3.3 50.5 - - + -
67P PHE* 3.5 37.5 - + + -
68P GLN* 3.1 23.7 - - + +
1270P CDL 3.8 11.2 - - - -
8W LYS* 2.9 40.7 + - + +
9W GLN 3.8 0.9 - - - +
11W LEU* 1.3 94.5 - - + +
13W GLN* 1.3 60.1 + - - +
14W GLU 3.5 0.2 - - - -
20W VAL* 5.0 1.1 - - + -
23W LYS* 3.0 37.3 + - + +
24W GLY* 3.6 25.4 - - - -
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Residues in contact with GLN 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P PHE 2.7 28.5 + - - +
68P GLN* 3.9 16.8 - - + +
14S THR* 2.8 25.8 + - - +
15S GLY* 4.5 6.6 + - - -
9W GLN* 3.0 20.6 + - - +
10W LYS* 3.0 6.0 + - - +
12W PHE* 1.3 80.5 - - - +
14W GLU* 1.3 53.3 + - - +
15W ASP* 2.8 23.0 + - - +
23W LYS* 4.0 5.0 + - - +
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Residues in contact with GLU 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W LYS* 2.8 16.3 + - + +
11W LEU* 3.2 33.9 + - - +
13W GLN* 1.3 71.5 - - - +
15W ASP* 1.3 54.2 + - - +
16W ASN* 2.7 40.4 + - + +
23W LYS* 3.1 15.9 - - - -
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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