Contacts of the helix formed by residues 6 - 19 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ASP* 3.4 17.3 - - - +
42I ASN 4.8 0.2 - - - +
43I PHE* 4.2 15.3 - - + -
3L GLN 5.7 1.8 + - - -
4L GLY* 3.5 8.7 - - - -
5L GLY* 1.3 82.6 - - - +
7L GLY* 1.3 63.6 + - - +
9L GLN* 2.9 24.4 + - + +
10L ASP* 3.2 40.1 + - - +
42L ASN* 2.9 19.9 + - - +
58L LYS* 4.8 0.5 + - - -
27Z U 2.7 30.8 + - - +
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Residues in contact with GLY 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP* 3.9 2.2 + - - +
3L GLN* 6.2 4.0 - - - -
4L GLY 5.3 0.8 - - - -
5L GLY* 3.5 5.7 + - - -
6L GLN* 1.3 76.0 - - - +
8L LEU* 1.3 63.1 + - - +
10L ASP* 4.0 2.6 - - - +
11L TYR* 3.1 26.8 + - - +
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Residues in contact with LEU 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I SER* 3.2 30.5 - - - +
40I PHE* 4.3 9.6 - - - +
41I ASP* 3.6 17.6 + - + +
44I THR* 3.3 23.8 - - - +
46I LEU* 4.1 23.1 - - + +
55I LEU* 3.7 20.0 - - + -
6L GLN 3.5 0.6 - - - -
7L GLY* 1.3 74.6 - - - +
9L GLN* 1.3 56.2 + - - +
11L TYR* 4.1 8.4 - - + +
12L TYR* 3.2 29.9 + - + +
72L LEU* 5.3 5.8 - - + -
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Residues in contact with GLN 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP* 3.1 14.7 + - - +
43I PHE* 4.2 5.3 - - - -
44I THR* 3.4 28.8 - - + +
55I LEU* 4.7 5.8 - - + +
57I PHE* 3.4 26.5 - - - -
6L GLN* 2.9 28.2 + - + +
8L LEU* 1.3 74.9 - - - +
10L ASP* 1.3 73.2 + - - +
12L TYR* 4.3 4.0 - - - -
13L LEU* 2.9 39.8 + - - +
58L LYS* 3.5 17.6 + - - +
27Z U 3.1 23.8 + - - +
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Residues in contact with ASP 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 3.2 40.4 + - - +
7L GLY* 3.5 3.6 + - - +
9L GLN* 1.3 89.9 + - - +
11L TYR* 1.3 63.4 + - - +
14L ASN* 3.2 23.7 + - - +
40L PHE* 3.5 21.5 - - + -
42L ASN* 5.0 2.8 - - - +
58L LYS* 4.9 2.8 + - - -
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Residues in contact with TYR 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L GLY 3.1 18.0 + - - +
8L LEU* 4.1 9.2 - - + +
10L ASP* 1.3 76.2 - - - +
12L TYR* 1.3 64.7 + + + +
14L ASN* 3.2 7.5 + - + +
15L GLN* 2.9 58.5 + - - +
18L LYS* 5.3 4.0 - - - -
70L VAL* 4.9 2.2 - - + -
71L ALA* 3.2 29.9 + - - +
72L LEU* 3.4 24.9 + - + -
73L ASN* 3.9 32.5 + - + +
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Residues in contact with TYR 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I LEU* 3.6 30.8 - - + +
53I GLN* 2.8 36.4 + - - +
55I LEU* 3.6 34.2 - - + +
8L LEU* 3.2 22.5 + - + +
9L GLN 3.9 2.9 - - - +
11L TYR* 1.3 85.5 - + + +
13L LEU* 1.3 62.1 + - - +
15L GLN* 3.4 4.8 + - - +
16L LEU* 3.0 54.9 + - + +
64L PHE* 5.0 2.5 - - + -
66L PRO* 3.3 24.5 - - + +
70L VAL* 3.7 19.8 - - + +
72L LEU* 4.9 5.6 - - + -
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Residues in contact with LEU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU* 4.7 8.5 - - + -
57I PHE* 5.2 2.2 - - + -
9L GLN* 2.9 36.6 + - - +
12L TYR* 1.3 77.1 - - - +
14L ASN* 1.3 62.0 + - - +
16L LEU* 3.7 14.2 + - + +
17L ARG* 3.2 21.5 + - - +
37L VAL* 3.8 12.7 - - + +
40L PHE* 3.5 37.3 - - + -
45L VAL* 4.3 8.7 - - + -
58L LYS* 4.2 14.4 - - - +
64L PHE* 3.7 41.1 - - + -
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Residues in contact with ASN 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ASP 3.2 20.5 + - - +
11L TYR* 3.2 8.4 + - + +
12L TYR 3.2 0.4 - - - -
13L LEU* 1.3 75.8 - - - +
15L GLN* 1.3 56.0 + - - +
17L ARG* 2.4 36.6 + - - +
18L LYS* 2.7 60.2 + - - +
40L PHE* 3.6 13.2 - - + -
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Residues in contact with GLN 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L TYR* 2.9 46.4 + - + +
12L TYR 3.7 1.1 - - - +
14L ASN* 1.3 77.2 + - - +
16L LEU* 1.3 56.6 + - - +
18L LYS* 3.2 29.4 + - - +
19L GLU* 2.9 62.8 + - + +
21L ILE* 4.5 3.3 - - + +
70L VAL* 3.6 30.1 - - + -
71L ALA* 4.5 12.4 - - - +
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Residues in contact with LEU 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L TYR* 3.0 40.0 + - + +
13L LEU* 3.8 11.2 - - + +
15L GLN* 1.3 75.6 - - - +
17L ARG* 1.3 61.7 + - - +
20L LYS* 3.3 3.3 + - - -
21L ILE* 3.2 51.7 + - + +
23L ALA* 4.7 7.9 - - + -
36L ARG* 5.7 0.2 - - - +
37L VAL* 4.0 21.7 + - + +
64L PHE* 4.1 24.9 - - + -
66L PRO* 4.0 16.4 - - + -
70L VAL* 3.6 23.3 - - + -
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Residues in contact with ARG 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LEU 3.2 12.6 + - - +
14L ASN* 2.4 43.4 + - - +
16L LEU* 1.3 78.6 - - - +
18L LYS* 1.3 91.7 + - - +
20L LYS* 3.5 14.9 + - - +
37L VAL* 3.5 30.6 - - + +
38L VAL 3.3 23.4 + - - +
39L SER* 4.4 7.8 - - - +
40L PHE* 4.5 7.9 - - - -
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Residues in contact with LYS 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L TYR* 5.3 3.8 - - - -
14L ASN* 2.7 37.9 + - - +
15L GLN* 3.2 32.5 + - - +
17L ARG* 1.3 101.1 - - - +
19L GLU* 1.3 61.5 + - + +
20L LYS* 3.1 12.2 + - - +
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Residues in contact with GLU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L GLN* 2.9 48.3 + - + +
18L LYS* 1.3 79.3 - - + +
20L LYS* 1.3 69.3 + - - +
21L ILE* 3.0 20.8 + - + +
68L LYS* 5.7 6.1 + - - +
71L ALA* 5.4 4.0 - - - +
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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