Contacts of the helix formed by residues 6 - 19 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 5.5 0.2 - - - -
3A GLN* 2.4 49.7 + - + +
4A GLY 3.2 2.6 + - - +
5A GLY* 1.3 73.3 - - - +
7A GLY* 1.3 61.7 + - - +
8A LEU 3.5 1.6 - - - -
9A GLN* 3.3 17.1 - - - +
10A ASP* 3.2 38.0 + - - +
42A ASN* 3.5 15.4 + - - +
58A LYS* 5.3 0.2 + - - -
41B ASP* 3.3 11.2 - - - +
43B PHE* 4.1 14.6 - - + -
18R U 2.8 41.3 + - - +
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Residues in contact with GLY 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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2A LYS* 3.6 32.5 - - - +
5A GLY* 3.4 5.3 + - - -
6A GLN* 1.3 74.3 - - - +
8A LEU* 1.3 65.8 + - - +
10A ASP* 3.4 3.3 + - - +
11A TYR* 3.1 26.8 + - - +
41B ASP* 4.1 1.2 - - - +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN 3.5 0.2 - - - -
7A GLY* 1.3 75.8 - - - +
9A GLN* 1.3 55.7 + - - +
11A TYR* 3.8 6.1 + - + +
12A TYR* 3.2 28.4 + - + +
72A LEU* 4.2 20.6 - - + -
39B SER* 3.7 32.3 - - - +
40B PHE* 4.1 8.1 - - - +
41B ASP* 3.9 16.2 + - + +
44B THR* 3.2 25.1 - - - +
46B LEU* 4.2 21.5 - - + +
55B LEU* 3.8 19.1 - - + -
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Residues in contact with GLN 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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6A GLN* 3.3 24.9 - - - +
7A GLY 3.2 0.2 - - - -
8A LEU* 1.3 77.6 - - - +
10A ASP* 1.3 69.2 + - - +
11A TYR 3.2 0.2 - - - -
12A TYR* 4.6 3.1 - - - -
13A LEU* 3.1 39.0 + - + +
58A LYS* 3.2 16.9 + - - +
41B ASP* 3.1 19.4 + - - +
43B PHE* 4.4 3.8 - - - +
44B THR* 3.5 21.2 - - + +
55B LEU* 5.1 2.7 - - + -
57B PHE* 3.2 26.8 - - + -
18R U 2.6 31.2 + - - +
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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
----------------------------------------------------------
2A LYS* 5.8 3.1 - - - -
3A GLN* 5.5 6.4 + - - +
6A GLN* 3.2 34.9 + - - +
7A GLY* 4.1 2.7 - - - +
9A GLN* 1.3 90.9 - - - +
11A TYR* 1.3 59.0 + - - +
14A ASN* 3.1 26.0 + - - +
40A PHE* 3.9 20.8 - - + -
42A ASN* 5.3 2.1 - - - +
58A LYS* 5.3 2.1 + - - -
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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
----------------------------------------------------------
7A GLY 3.1 18.2 + - - +
8A LEU* 4.0 7.0 - - + +
10A ASP* 1.3 75.8 - - - +
12A TYR* 1.3 64.3 + + + +
14A ASN* 3.2 8.2 + - + +
15A GLN* 2.9 67.5 + - + +
70A VAL* 4.3 3.8 - - + -
71A ALA* 3.2 32.7 + - - +
72A LEU* 4.2 16.5 + - + -
73A ASN* 3.3 28.7 + - - -
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Residues in contact with TYR 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 LEU* 3.2 21.8 + - + +
9A GLN 4.0 2.7 - - - +
11A TYR* 1.3 85.0 - + + +
13A LEU* 1.3 63.8 + - - +
15A GLN* 3.3 4.8 + - - +
16A LEU* 3.1 55.2 + - + +
64A PHE* 4.9 2.2 - - + -
66A PRO* 3.3 21.4 - - + +
70A VAL* 3.9 18.1 - - + +
72A LEU* 5.2 4.7 - - + -
46B LEU* 3.5 32.9 - - + +
53B GLN* 2.5 39.2 + - - +
55B LEU* 3.5 37.5 + - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.1 35.6 + - + +
12A TYR* 1.3 79.3 - - - +
14A ASN* 1.3 61.4 + - - +
16A LEU* 3.9 14.1 + - + +
17A ARG* 3.4 16.8 + - - +
37A VAL* 4.0 9.3 - - + +
40A PHE* 3.3 37.9 - - + -
45A VAL* 4.6 9.0 - - + -
58A LYS* 4.2 22.7 - - - +
64A PHE* 3.7 37.7 - - + -
55B LEU* 4.4 8.3 - - + -
57B PHE* 4.9 5.2 - - + -
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Residues in contact with ASN 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 ASP 3.1 20.3 + - - +
11A TYR* 3.2 9.2 + - - +
12A TYR 3.1 0.6 - - - -
13A LEU* 1.3 77.6 - - - +
15A GLN* 1.3 58.6 + - + +
17A ARG* 2.2 45.2 + - - +
18A LYS* 2.7 54.1 + - - +
40A PHE* 3.7 9.2 - - + -
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Residues in contact with GLN 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* 2.9 61.9 + - + +
12A TYR 3.3 1.8 + - - +
14A ASN* 1.3 78.3 - - - +
16A LEU* 1.3 55.6 + - - +
18A LYS* 4.1 26.0 - - - +
19A GLU* 2.6 62.2 + - + +
21A ILE* 5.2 1.1 - - + -
70A VAL* 3.7 22.8 - - + +
71A ALA* 5.9 1.0 + - - +
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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 TYR* 3.1 39.0 + - + +
13A LEU* 4.0 13.9 - - + +
15A GLN* 1.3 77.5 - - - +
17A ARG* 1.3 58.5 + - - +
20A LYS* 3.3 6.1 + - - -
21A ILE* 3.2 46.8 + - + +
23A ALA* 4.7 7.6 - - + -
36A ARG* 5.6 0.3 - - - +
37A VAL* 4.2 17.2 + - + +
64A PHE* 4.2 25.1 - - + -
66A PRO* 3.7 22.4 - - + -
70A VAL* 3.7 23.1 - - + -
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Residues in contact with ARG 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 LEU 3.4 11.5 + - - +
14A ASN* 2.2 55.1 + - - +
15A GLN 3.1 0.4 - - - -
16A LEU* 1.3 78.5 - - - +
18A LYS* 1.3 84.3 + - - +
20A LYS* 3.5 23.1 + - - +
37A VAL* 3.3 31.8 - - + +
38A VAL* 3.2 23.5 + - - +
39A SER* 4.5 6.5 - - - +
40A PHE* 4.8 6.6 - - - -
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Residues in contact with LYS 18 (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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14A ASN* 2.7 44.4 + - - +
15A GLN* 3.9 21.1 - - - +
17A ARG* 1.3 99.0 - - - +
19A GLU* 1.3 67.7 + - + +
20A LYS* 3.1 9.8 + - - +
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Residues in contact with GLU 19 (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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15A GLN* 2.6 49.5 + - + +
18A LYS* 1.3 80.0 + - + +
20A LYS* 1.3 67.0 + - - +
21A ILE* 3.0 23.1 + - + +
68A LYS* 6.2 1.1 - - + -
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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