Contacts of the helix formed by residues 2 - 17 (chain A) in PDB entry 4ENM
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 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 75.9 - - - +
3A MET* 1.3 66.1 + - - +
4A ASP* 2.7 57.4 + - - +
5A GLU* 2.8 50.8 + - + +
6A PHE* 3.0 11.3 + - - +
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Residues in contact with MET 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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1A MET* 3.6 15.9 + - + +
2A ARG* 1.3 72.6 - - - +
4A ASP* 1.3 59.0 - - - +
5A GLU 3.0 0.2 + - - -
6A PHE* 3.1 27.3 - - + +
7A TYR* 2.9 40.8 + - + -
34A MET* 6.3 0.4 - - - -
37A TYR* 3.6 29.2 - - + +
40A GLN* 5.4 0.4 - - - -
23C A 3.7 26.7 - - - +
24C T 3.6 35.9 - - - +
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Residues in contact with ASP 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 ARG* 2.7 51.6 + - - +
3A MET* 1.3 78.1 - - - +
5A GLU* 1.3 58.3 + - - +
7A TYR* 4.0 8.9 - - - +
8A THR* 2.6 35.0 + - - -
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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* 3.8 17.6 - - + -
2A ARG* 2.8 67.7 + - + +
4A ASP* 1.3 82.3 + - - +
6A PHE* 1.3 55.4 + - - +
8A THR* 2.9 8.4 + - - -
9A LYS* 2.7 43.5 + - + +
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Residues in contact with PHE 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* 4.0 9.9 - - - -
2A ARG 3.0 7.8 + - - +
3A MET* 3.1 21.5 - - + +
5A GLU* 1.3 75.3 - - - +
7A TYR* 1.3 90.2 + + - +
9A LYS* 2.7 22.6 + - - +
10A VAL* 2.7 37.8 + - + +
29A ALA* 5.2 1.1 - - - -
32A VAL* 4.0 17.3 - - + -
34A MET* 4.0 28.7 - - + -
37A TYR* 3.8 28.3 - + + -
40A GLN* 3.5 31.6 - - + -
41A VAL* 4.1 8.1 - - + -
44A ALA* 5.3 0.4 - - + -
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Residues in contact with TYR 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 MET* 2.9 33.1 + - + +
4A ASP* 4.0 8.3 - - - +
6A PHE* 1.3 100.9 - + - +
8A THR* 1.3 64.5 + - - +
10A VAL* 3.5 6.3 + - - +
11A TYR* 3.1 48.5 + + + -
40A GLN* 4.7 4.7 - - + -
43A GLN* 2.7 34.0 + - - +
44A ALA* 4.4 15.7 - - + -
47A HIS* 3.8 26.2 + + + -
24C T 3.5 13.9 + - - -
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Residues in contact with THR 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 ASP* 2.6 20.2 + - - -
5A GLU* 2.9 10.8 + - - -
7A TYR* 1.3 80.4 - - - +
9A LYS* 1.3 66.4 + - + +
11A TYR* 3.1 9.3 + - + +
12A ASP* 2.9 39.1 + - - +
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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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1A MET* 3.0 29.7 - - + +
5A GLU* 2.7 34.9 + - + +
6A PHE* 2.7 10.1 + - - +
8A THR* 1.3 72.3 - - + +
10A VAL* 1.3 63.8 + - - +
12A ASP* 3.1 14.7 + - - +
13A ALA* 3.0 21.1 + - - +
32A VAL* 3.8 32.5 + - + +
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Residues in contact with VAL 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 PHE* 2.7 57.3 + - + +
7A TYR 3.7 4.9 - - - +
9A LYS* 1.3 72.6 - - - +
11A TYR* 1.3 66.0 + - - +
13A ALA* 2.7 14.2 + - - +
14A VAL* 2.9 18.6 + - + +
28A ILE* 4.0 10.3 - - + -
32A VAL* 4.2 13.0 - - + -
41A VAL* 3.8 16.8 - - + -
44A ALA* 4.1 9.0 - - + -
45A MET* 3.5 30.5 - - + -
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Residues in contact with TYR 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 TYR* 3.1 35.1 - + + -
8A THR* 3.1 8.4 + - - +
10A VAL* 1.3 77.2 - - + +
12A ASP* 1.3 65.7 + - - +
14A VAL* 3.2 4.8 + - - +
15A CYS* 3.0 31.2 + - - -
44A ALA* 2.8 45.4 + - + -
45A MET* 4.1 11.0 - - + -
47A HIS* 4.4 4.3 - - - +
48A LEU* 3.5 40.6 + - + +
54A VAL* 4.7 15.0 - - + -
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Residues in contact with ASP 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 THR* 2.9 36.0 + - - +
9A LYS* 3.2 14.8 - - - +
11A TYR* 1.3 78.3 - - - +
13A ALA* 1.3 61.9 + - - +
15A CYS* 3.6 7.2 + - - +
16A GLU* 3.2 28.7 + - - +
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Residues in contact with ALA 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 3.0 10.0 + - - +
10A VAL 2.7 14.3 + - - +
12A ASP* 1.3 69.3 - - - +
14A VAL* 1.3 67.6 + - - +
16A GLU* 2.8 32.9 + - - +
17A ILE* 3.6 5.5 + - - +
28A ILE* 4.1 15.7 - - + -
31A TYR* 3.3 30.7 - - + -
32A VAL* 4.1 9.0 - - + -
106A TRP* 4.6 3.3 - - - -
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Residues in contact with VAL 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 VAL* 2.9 22.5 + - + +
11A TYR* 3.6 6.3 - - - +
13A ALA* 1.3 71.7 - - - +
15A CYS* 1.3 55.0 + - - +
17A ILE* 2.7 45.4 + - + +
28A ILE* 4.8 9.4 - - + -
45A MET* 3.8 26.7 - - + -
54A VAL* 4.2 8.5 - - + -
55A PRO* 3.4 38.2 - - + +
56A TRP* 4.3 2.0 - - - +
59A VAL* 3.7 21.3 - - + -
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Residues in contact with CYS 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 TYR* 3.0 19.6 + - - +
12A ASP* 3.8 7.6 - - - +
14A VAL* 1.3 78.8 - - - +
16A GLU* 1.3 60.7 + - + +
17A ILE 3.2 5.1 + - - +
53A HIS 4.8 3.4 - - - -
54A VAL* 3.8 22.4 - - - -
55A PRO* 3.6 27.2 - - - +
58A ARG* 5.5 1.2 + - - -
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Residues in contact with GLU 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 ASP* 3.2 27.4 - - - +
13A ALA* 2.8 17.3 + - - +
15A CYS* 1.3 77.9 - - + +
17A ILE* 1.3 61.2 + - - +
18A PRO* 3.1 10.0 - - - +
31A TYR* 2.9 31.0 + - - -
106A TRP* 3.8 20.9 + - + -
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Residues in contact with ILE 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 ALA 3.9 3.1 - - - +
14A VAL* 2.7 48.3 + - + +
15A CYS 4.2 3.3 - - - +
16A GLU* 1.3 68.6 - - - +
18A PRO* 1.3 76.4 - - + +
19A TYR 3.5 0.5 + - - -
21A LYS* 4.0 2.7 - - + -
22A VAL* 3.8 29.8 - - - +
23A SER* 3.3 30.3 - - - -
28A ILE* 4.4 6.3 - - + -
58A ARG* 2.9 45.9 + - + +
59A VAL* 4.4 2.7 - - + -
106A TRP* 4.2 13.5 - - + -
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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