Contacts of the helix formed by residues 6 - 19 (chain E) in PDB entry 4NL3
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 GLN 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E GLN* 3.7 14.5 - - - +
4E GLY 2.7 22.2 - - - +
5E GLY* 1.3 82.0 - - - +
7E GLY* 1.3 61.3 + - - +
8E LEU 3.5 1.6 - - - -
9E GLN* 3.5 13.5 - - - +
10E ASP* 3.0 49.3 + - - +
42E ASN* 3.5 12.3 + - - +
58E LYS* 5.0 2.0 - - - +
41F ASP* 3.2 16.8 - - - +
43F PHE* 4.1 13.7 - - + -
29Z U 3.0 29.5 + - - +
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Residues in contact with GLY 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLY* 3.6 8.9 + - - -
5E GLY 3.8 0.8 - - - -
6E GLN* 1.3 74.1 - - - +
8E LEU* 1.3 56.9 + - - +
10E ASP* 3.3 3.1 + - - +
11E TYR* 2.8 38.6 + - - +
41F ASP* 4.2 1.6 - - - +
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Residues in contact with LEU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN 3.5 0.4 - - - -
7E GLY* 1.3 74.3 - - - +
9E GLN* 1.3 56.6 + - - +
11E TYR* 4.0 6.1 - - + +
12E TYR* 3.1 29.6 + - + +
72E LEU* 4.6 12.6 - - + -
39F SER* 3.6 33.2 - - - +
40F PHE* 4.1 4.5 - - - +
41F ASP* 3.9 19.6 - - + +
44F THR* 3.2 31.4 - - - +
46F LEU* 4.2 24.7 - - + +
55F LEU* 3.7 19.5 - - + -
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Residues in contact with GLN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.5 32.7 - - - +
7E GLY 3.2 0.4 - - - -
8E LEU* 1.3 77.4 - - - +
10E ASP* 1.3 62.0 + - - +
12E TYR* 3.9 3.5 - - - +
13E LEU* 3.1 42.3 + - + +
40E PHE* 5.9 0.2 - - + -
58E LYS* 2.7 32.3 + - - -
41F ASP* 3.2 15.6 + - - +
43F PHE* 4.1 6.2 - - - +
44F THR* 3.4 28.3 - - + +
55F LEU* 5.0 2.9 - - + -
57F PHE* 3.3 16.2 - - + -
29Z U 3.4 12.6 - - - +
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Residues in contact with ASP 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E GLN 4.8 5.0 - - - +
4E GLY 5.5 0.2 + - - -
6E GLN* 3.0 47.8 + - - +
7E GLY* 3.3 4.2 + - - +
9E GLN* 1.3 81.0 + - - +
11E TYR* 1.3 62.2 + - - +
14E ASN* 3.2 23.6 + - - +
40E PHE* 3.8 19.2 - - + -
58E LYS* 5.2 1.4 + - - -
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Residues in contact with TYR 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLY 2.8 18.8 + - - +
8E LEU* 4.0 8.3 - - + +
10E ASP* 1.3 77.0 - - - +
12E TYR* 1.3 68.0 + + + +
14E ASN* 3.3 6.3 + - + +
15E GLN* 3.1 55.6 + - + +
18E LYS* 5.7 0.4 - - - -
70E VAL* 4.3 5.4 - - + -
71E ALA* 2.2 38.2 + - - +
72E LEU* 3.9 29.3 + - + -
73E ASN* 5.4 4.5 - - + -
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Residues in contact with TYR 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.1 21.2 + - + +
9E GLN 3.9 0.9 - - - +
10E ASP 3.4 0.4 - - - -
11E TYR* 1.3 85.4 - + + +
13E LEU* 1.3 62.7 + - - +
15E GLN* 3.4 5.4 + - - +
16E LEU* 3.1 55.9 + - + +
64E PHE* 4.9 2.5 - - + -
66E PRO* 3.1 25.7 - - + +
70E VAL* 3.7 17.7 - - + -
72E LEU* 5.7 2.5 - - + -
46F LEU* 3.6 31.9 - - + +
53F GLN* 2.9 35.8 + - - +
55F LEU* 3.4 39.1 - - + +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 3.1 27.8 + - + +
12E TYR* 1.3 78.4 - - - +
14E ASN* 1.3 57.6 + - - +
16E LEU* 3.7 15.3 + - + +
17E ARG* 3.1 25.6 + - - +
37E VAL* 3.9 13.7 - - + +
40E PHE* 3.4 44.1 - - + -
45E VAL* 4.4 10.1 - - + -
58E LYS* 4.3 14.4 - - - -
64E PHE* 3.8 39.7 - - + -
55F LEU* 4.7 7.6 - - + -
57F PHE* 5.1 2.2 - - + -
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Residues in contact with ASN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASP 3.2 19.2 + - - +
11E TYR* 3.3 7.9 + - + +
12E TYR 3.1 0.8 - - - -
13E LEU* 1.3 77.2 - - - +
15E GLN* 1.3 53.1 + - - +
17E ARG* 2.4 36.1 + - - +
18E LYS* 2.6 65.3 + - - +
40E PHE* 3.7 12.5 - - + -
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Residues in contact with GLN 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 3.1 59.1 + - + +
12E TYR 3.8 0.9 - - - +
14E ASN* 1.3 72.7 + - - +
16E LEU* 1.3 61.8 + - - +
18E LYS* 2.8 33.0 + - - +
19E GLU* 2.9 59.5 + - + +
21E ILE* 3.9 1.5 - - - +
70E VAL* 3.6 25.8 - - + +
71E ALA* 4.8 6.7 + - - +
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TYR* 3.1 41.5 + - + +
13E LEU* 3.7 14.6 - - + +
15E GLN* 1.3 77.5 - - - +
17E ARG* 1.3 61.0 + - - +
20E LYS* 3.5 3.1 + - - -
21E ILE* 3.4 62.8 + - + +
23E ALA* 4.6 8.3 - - + -
37E VAL* 4.1 17.9 + - + +
64E PHE* 4.1 26.2 - - + -
66E PRO* 3.9 10.1 - - + -
70E VAL* 3.7 16.4 - - + -
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Residues in contact with ARG 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 3.1 14.8 + - - +
14E ASN* 2.4 41.7 + - - +
16E LEU* 1.3 76.0 - - - +
18E LYS* 1.3 90.8 + - - +
20E LYS* 3.5 10.6 + - - +
37E VAL* 3.4 24.3 - - + +
38E VAL 3.2 29.3 + - - +
39E SER* 4.4 6.7 - - - +
40E PHE* 4.6 7.9 - - - -
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Residues in contact with LYS 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 5.7 0.8 - - - -
14E ASN* 2.6 38.3 + - - +
15E GLN* 2.8 35.0 + - - +
17E ARG* 1.3 98.6 - - - +
19E GLU* 1.3 64.9 + - + +
20E LYS* 3.0 11.6 + - - +
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Residues in contact with GLU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E GLN* 2.9 42.6 + - - +
18E LYS* 1.3 74.5 - - + +
20E LYS* 1.3 68.7 + - - +
21E ILE* 2.9 17.1 + - + +
68E LYS* 5.6 8.6 + - - +
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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