Contacts of the helix formed by residues 3 - 17 (chain A) in PDB entry 2N57
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 3.8 8.7 - - - +
2A SER* 1.3 78.6 - - - +
4A THR* 1.3 68.3 + - - +
6A GLU* 4.3 2.0 - - - +
7A ARG* 3.5 26.0 + - - +
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Residues in contact with THR 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 SER* 4.7 0.2 - - - -
3A ASP* 1.3 78.0 - - - +
5A ALA* 1.3 68.0 + - - +
7A ARG* 3.0 5.5 + - - +
8A VAL* 2.8 35.7 + - + +
51A PHE* 4.4 10.1 - - + -
70A VAL* 3.5 31.0 - - + +
73A ILE* 4.3 9.0 - - + -
74A ASP* 2.8 45.4 + - + +
77A SER* 5.9 0.3 - - - -
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Residues in contact with ALA 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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2A SER* 3.3 26.3 - - - +
3A ASP 3.5 0.2 - - - -
4A THR* 1.3 78.3 - - - +
6A GLU* 1.3 64.5 + - + +
8A VAL* 3.2 0.5 + - - +
9A LYS* 2.8 52.8 + - - +
70A VAL* 3.4 18.8 - - + +
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Residues in contact with GLU 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 4.9 7.8 + - - +
2A SER* 3.2 30.7 + - - +
3A ASP* 4.3 3.1 - - - +
4A THR 3.3 0.2 - - - -
5A ALA* 1.3 77.9 - - + +
7A ARG* 1.3 57.5 + - - +
9A LYS* 4.0 11.7 - - - +
10A LYS* 2.9 44.0 + - + +
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Residues in contact with ARG 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 ASP 3.5 15.8 + - - +
4A THR 3.0 9.1 + - - +
6A GLU* 1.3 76.1 - - - +
8A VAL* 1.3 66.6 + - - +
10A LYS* 3.1 7.4 + - - +
11A ILE* 2.9 35.0 + - + +
51A PHE* 3.4 38.6 - - + -
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Residues in contact with VAL 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 THR* 2.8 29.1 + - + +
5A ALA 3.8 0.2 - - - +
7A ARG* 1.3 72.6 - - - +
9A LYS* 1.3 66.1 + - - +
11A ILE* 3.1 9.6 + - - +
12A VAL* 2.9 37.6 + - + +
29A PHE* 5.6 0.9 - - + -
47A PHE* 4.1 15.3 - - + -
51A PHE* 4.8 4.7 - - + -
66A VAL* 4.8 4.3 - - + -
69A ALA* 4.8 3.1 - - + -
70A VAL* 3.4 40.2 - - + +
73A ILE* 3.5 29.4 - - + -
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Residues in contact with LYS 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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5A ALA* 2.8 52.1 + - - +
6A GLU* 4.0 13.7 - - - +
8A VAL* 1.3 72.1 - - + +
10A LYS* 1.3 58.4 + - - +
12A VAL* 3.1 5.1 + - - +
13A VAL* 2.8 36.9 + - + +
20A ALA* 5.6 4.3 - - + +
23A VAL* 2.9 54.7 + - + +
24A THR* 4.3 10.1 - - - +
25A GLU 4.7 2.0 - - - +
66A VAL* 4.4 10.8 - - + +
70A VAL* 5.4 0.7 - - - -
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Residues in contact with LYS 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 GLU* 2.9 34.7 + - + +
7A ARG* 3.3 6.5 - - - +
9A LYS* 1.3 76.7 - - - +
11A ILE* 1.3 59.0 + - + +
13A VAL* 3.1 10.2 + - + +
14A GLU* 2.9 37.7 + - - +
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Residues in contact with ILE 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 ARG* 2.9 31.5 + - + +
8A VAL* 3.6 5.2 - - - +
10A LYS* 1.3 76.8 - - + +
12A VAL* 1.3 54.2 + - - +
14A GLU* 3.4 3.8 + - - +
15A HIS* 2.8 72.2 + - + +
46A ALA* 5.3 0.2 - - + -
47A PHE* 3.5 31.9 - - + -
50A GLU* 3.8 28.5 - - + +
51A PHE* 4.2 17.9 - - + -
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Residues in contact with VAL 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 VAL* 2.9 36.0 + - + +
9A LYS* 3.1 10.5 + - - +
11A ILE* 1.3 78.4 - - - +
13A VAL* 1.3 54.4 + - - +
15A HIS* 4.4 3.6 - - - -
16A LEU* 2.8 65.5 + - + +
18A VAL* 5.0 1.8 - - + -
23A VAL* 4.6 17.3 - - + -
29A PHE* 4.1 23.3 - - + -
33A LEU* 5.2 0.7 - - + -
43A LEU* 4.4 6.3 - - + -
47A PHE* 3.5 23.3 - - + -
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Residues in contact with VAL 13 (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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9A LYS 2.8 21.6 + - - +
10A LYS* 3.6 9.4 - - + +
12A VAL* 1.3 76.3 - - - +
14A GLU* 1.3 58.2 + - - +
17A GLY* 2.9 27.9 + - - +
18A VAL* 2.9 27.1 - - - +
20A ALA* 3.7 37.5 - - + +
23A VAL* 4.0 12.1 - - + -
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Residues in contact with GLU 14 (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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10A LYS* 2.9 22.4 + - - +
11A ILE* 4.0 5.5 - - - +
13A VAL* 1.3 77.1 - - - +
15A HIS* 1.3 73.7 + - + +
17A GLY* 4.2 2.3 + - - -
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Residues in contact with HIS 15 (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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11A ILE* 2.8 51.4 + - + +
12A VAL* 4.1 3.4 - - - +
14A GLU* 1.3 90.8 + - + +
16A LEU* 1.3 68.8 + - + +
17A GLY 3.6 0.3 + - - -
43A LEU* 4.8 13.2 - - + +
46A ALA* 4.0 23.9 - - + +
50A GLU* 4.8 7.7 + - + -
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Residues in contact with LEU 16 (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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12A VAL* 2.8 42.2 + - + +
15A HIS* 1.3 80.4 - - + +
17A GLY* 1.3 62.4 + - - +
18A VAL* 3.4 20.4 - - + +
29A PHE* 4.6 3.8 - - + -
33A LEU* 3.2 35.4 - - + -
39A ASP* 3.7 24.7 - - - +
43A LEU* 4.2 16.2 - - + -
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Residues in contact with GLY 17 (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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13A VAL* 2.9 19.5 + - - -
14A GLU 4.9 2.7 - - - -
15A HIS 3.3 2.0 - - - -
16A LEU* 1.3 79.6 - - - +
18A VAL* 1.3 63.4 + - - +
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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