Contacts of the helix formed by residues 6 - 19 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASP* 3.4 16.4 - - - +
42A ASN 4.6 0.2 - - - +
43A PHE* 3.7 22.6 - - + -
3D GLN* 3.8 26.3 + - - +
4D GLY* 3.4 2.9 - - - -
5D GLY* 1.3 72.6 - - - +
7D GLY* 1.3 63.8 - - - +
9D GLN* 4.0 5.1 + - - +
10D ASP* 3.6 39.9 + - - +
42D ASN* 4.1 13.3 + - - +
58D LYS* 5.2 0.2 + - - -
17R U 3.0 39.3 + - - +
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Residues in contact with GLY 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 3.8 1.4 - - - +
3D GLN* 5.9 5.8 - - - -
4D GLY 4.9 2.0 + - - -
5D GLY* 3.4 5.9 + - - -
6D GLN* 1.3 75.6 - - - +
8D LEU* 1.3 64.7 + - - +
9D GLN 3.3 0.2 + - - -
10D ASP* 4.3 1.5 - - - +
11D TYR* 3.2 26.8 + - - +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 3.8 28.9 - - - +
40A PHE* 4.1 6.1 - - - +
41A ASP* 3.5 19.3 + - + +
44A THR* 3.1 28.9 - - - +
46A LEU* 4.0 24.7 - - + +
55A LEU* 3.6 20.2 - - + -
7D GLY* 1.3 74.6 - - - +
9D GLN* 1.3 58.8 + - - +
11D TYR* 4.3 6.0 - - + +
12D TYR* 3.2 29.5 + - + +
72D LEU* 4.2 17.0 - - + -
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Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 2.8 15.2 + - - +
43A PHE* 3.3 26.3 - - - +
44A THR* 3.4 21.2 + - + +
55A LEU* 5.1 3.1 - - + -
57A PHE* 3.9 9.8 - - + -
6D GLN* 4.0 5.8 + - - +
7D GLY 3.3 0.2 - - - -
8D LEU* 1.3 77.3 - - - +
10D ASP* 1.3 70.8 + - - +
12D TYR* 3.5 3.7 + - - +
13D LEU* 3.1 36.4 + - + +
58D LYS* 2.2 42.6 + - - +
17R U 3.2 20.4 + - - +
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Residues in contact with ASP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.6 39.2 + - - +
7D GLY* 3.5 3.0 + - - +
9D GLN* 1.3 84.0 - - - +
11D TYR* 1.3 65.3 + - - +
14D ASN* 3.2 24.4 + - - +
40D PHE* 3.4 25.2 - - + -
42D ASN* 5.0 5.6 - - - +
58D LYS* 4.7 2.4 + - - -
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Residues in contact with TYR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY 3.2 16.7 + - - +
8D LEU* 4.3 6.1 - - + +
10D ASP* 1.3 80.7 - - - +
12D TYR* 1.3 65.7 + + + +
14D ASN* 3.4 7.9 + - + +
15D GLN* 3.1 54.9 + - + +
70D VAL* 5.1 1.8 - - + -
71D ALA* 3.1 32.2 + - - +
72D LEU* 4.2 12.0 + - + -
73D ASN* 3.6 32.2 + - - -
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Residues in contact with TYR 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.6 32.0 - - + +
53A GLN* 2.5 38.1 + - - +
55A LEU* 3.5 35.7 - - + +
8D LEU* 3.2 22.1 + - + +
9D GLN 3.9 3.1 - - - +
10D ASP 3.4 0.2 - - - -
11D TYR* 1.3 84.4 - + + +
13D LEU* 1.3 60.2 - - - +
15D GLN* 3.4 5.8 + - - +
16D LEU* 3.1 41.5 + - + +
64D PHE* 5.0 1.8 - - + -
66D PRO* 3.4 23.5 - - + +
70D VAL* 3.8 23.9 - - + +
72D LEU* 4.8 4.9 - - + -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 4.5 6.7 - - + -
57A PHE* 5.0 2.0 - - + -
9D GLN* 3.1 30.5 + - + +
12D TYR* 1.3 77.2 - - - +
14D ASN* 1.3 61.2 + - - +
16D LEU* 3.7 14.6 + - + +
17D ARG* 3.2 20.8 + - - +
37D VAL* 3.9 14.7 - - + +
40D PHE* 3.6 37.3 - - + -
45D VAL* 4.2 17.9 - - + -
58D LYS* 4.2 11.7 - - - -
64D PHE* 3.7 41.5 - - + -
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Residues in contact with ASN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASP 3.2 21.1 + - - +
11D TYR* 3.6 9.0 - - - +
12D TYR 3.2 0.6 - - - -
13D LEU* 1.3 76.7 - - - +
15D GLN* 1.3 55.2 + - + +
17D ARG* 2.5 34.3 + - - +
18D LYS* 2.6 57.6 + - - +
40D PHE* 3.7 17.0 - - + -
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.1 55.1 + - + +
12D TYR 3.8 0.4 - - - +
14D ASN* 1.3 75.8 + - - +
16D LEU* 1.3 57.7 + - - +
18D LYS* 2.5 37.9 + - - +
19D GLU* 2.4 63.8 + - + +
21D ILE* 5.1 0.7 - - - -
70D VAL* 3.6 24.5 - - + +
71D ALA* 4.9 6.0 + - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TYR* 3.1 37.5 + - + +
13D LEU* 3.8 12.3 - - + +
15D GLN* 1.3 74.9 - - - +
17D ARG* 1.3 56.9 + - - +
20D LYS* 3.1 20.6 + - - -
21D ILE* 3.2 45.2 + - + +
23D ALA* 4.7 8.1 - - + -
37D VAL* 4.0 29.5 + - + +
64D PHE* 4.1 20.6 - - + -
66D PRO* 4.0 11.9 - - + -
70D VAL* 3.6 20.4 - - + -
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU 3.2 11.9 + - - +
14D ASN* 2.5 41.7 + - - +
16D LEU* 1.3 78.3 - - - +
18D LYS* 1.3 91.3 + - - +
20D LYS* 3.6 16.6 + - - +
37D VAL* 3.4 22.6 - - + +
38D VAL* 3.2 29.2 + - - +
39D SER* 4.4 7.9 - - - +
40D PHE* 4.8 5.8 - - - -
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Residues in contact with LYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN* 2.6 42.6 + - - +
15D GLN* 2.5 41.0 + - - +
17D ARG* 1.3 93.9 - - - +
19D GLU* 1.3 64.4 + - + +
20D LYS* 3.1 9.6 + - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLN* 2.4 59.8 + - + +
18D LYS* 1.3 71.7 + - - +
20D LYS* 1.3 68.2 + - - +
21D ILE* 3.0 27.6 + - + +
68D LYS* 5.1 8.2 + - - -
70D VAL* 6.0 2.7 - - + -
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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