Contacts of the helix formed by residues 6 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B LYS* 5.0 0.2 - - - -
3B GLN* 3.6 38.4 + - + +
4B GLY 3.2 4.2 + - - +
5B GLY* 1.3 82.6 - - - +
7B GLY* 1.3 63.3 + - - +
8B LEU 3.4 0.9 - - - -
9B GLN* 4.1 5.0 + - - +
10B ASP* 3.1 45.4 + - - +
42B ASN* 3.4 12.5 + - - +
58B LYS* 5.2 0.5 + - - -
41J ASP* 3.2 17.3 - - - +
43J PHE* 4.5 11.1 - - + -
19R U 2.7 38.8 + - - +
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 4.3 22.2 - - - +
5B GLY* 3.9 1.2 - - - +
6B GLN* 1.3 76.4 - - - +
8B LEU* 1.3 53.8 + - - +
10B ASP* 3.3 2.7 + - - +
11B TYR* 2.7 39.6 + - - +
41J ASP* 4.3 2.0 - - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN 3.4 0.2 - - - -
7B GLY* 1.3 76.4 - - - +
9B GLN* 1.3 56.1 + - - +
11B TYR* 4.0 10.4 - - + +
12B TYR* 3.0 30.8 + - + +
72B LEU* 5.3 4.9 - - + -
39J SER* 3.7 32.1 - - - +
40J PHE* 4.1 4.9 - - - +
41J ASP* 3.9 18.4 - - + +
44J THR* 3.2 28.9 - - - +
46J LEU* 4.3 26.9 - - + +
55J LEU* 3.8 17.9 - - + -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 4.1 5.7 + - - -
7B GLY 3.3 0.6 - - - -
8B LEU* 1.3 78.1 - - - +
10B ASP* 1.3 68.7 + - - +
12B TYR* 4.0 2.9 - - - +
13B LEU* 3.0 42.9 + - + +
40B PHE* 6.1 0.2 - - - -
58B LYS* 2.2 41.7 + - - +
41J ASP* 3.2 17.0 + - - +
43J PHE* 3.6 20.0 - - - +
44J THR* 3.4 25.1 - - + +
55J LEU* 4.9 2.9 - - + -
57J PHE* 3.9 4.3 - - + -
19R U 3.3 23.0 + - - +
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 5.9 2.1 - - - +
6B GLN* 3.1 47.5 + - - +
7B GLY* 3.9 2.0 - - - +
9B GLN* 1.3 83.4 - - - +
11B TYR* 1.3 61.5 + - - +
14B ASN* 3.2 23.4 + - - +
40B PHE* 3.8 20.3 - - + -
42B ASN* 5.3 2.3 - - - +
58B LYS* 5.2 1.9 + - - -
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Residues in contact with TYR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLY 2.7 20.2 + - - +
8B LEU* 4.0 12.1 - - + +
10B ASP* 1.3 76.2 - - - +
12B TYR* 1.3 71.4 + + + +
14B ASN* 3.3 6.8 + - + +
15B GLN* 3.1 55.6 + - + +
18B LYS* 5.4 1.6 - - - -
70B VAL* 4.2 5.2 - - + -
71B ALA* 2.4 37.0 + - - +
72B LEU* 3.5 22.3 + - + -
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.0 24.6 + - + +
9B GLN 4.0 0.7 - - - +
11B TYR* 1.3 82.7 - + - +
13B LEU* 1.3 63.2 - - - +
14B ASN 3.3 0.2 + - - -
15B GLN* 3.3 6.9 + - - +
16B LEU* 3.2 39.4 + - + +
64B PHE* 5.0 2.0 - - + -
66B PRO* 3.3 24.9 - - + +
70B VAL* 3.6 27.4 - - + +
72B LEU* 5.9 1.3 - - + -
46J LEU* 3.6 32.9 - - + +
53J GLN* 2.8 35.5 + - - +
55J LEU* 3.6 37.6 + - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.0 41.4 + - + +
12B TYR* 1.3 77.9 - - - +
14B ASN* 1.3 62.0 + - - +
16B LEU* 3.7 13.4 + - + +
17B ARG* 3.3 21.3 + - - +
37B VAL* 4.0 13.2 - - + +
40B PHE* 3.5 39.6 - - + -
45B VAL* 4.4 8.1 - - + -
58B LYS* 4.2 9.4 - - - +
64B PHE* 3.7 41.5 - - + -
55J LEU* 4.6 7.0 - - + -
57J PHE* 5.0 1.8 - - + -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP 3.2 20.6 + - - +
11B TYR* 3.3 8.7 + - + +
12B TYR 3.1 0.4 - - - -
13B LEU* 1.3 77.7 - - - +
15B GLN* 1.3 53.4 + - - +
17B ARG* 2.3 37.3 + - - +
18B LYS* 2.7 64.6 + - - +
40B PHE* 3.9 12.4 - - + -
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.1 52.6 + - + +
12B TYR 3.3 3.6 + - - +
14B ASN* 1.3 74.2 - - - +
16B LEU* 1.3 58.8 + - - +
18B LYS* 2.6 32.7 + - - +
19B GLU* 2.9 57.6 + - + +
21B ILE* 4.2 2.0 - - - +
70B VAL* 3.5 27.3 - - + +
71B ALA* 4.9 9.9 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.2 34.3 + - + +
13B LEU* 3.8 11.2 - - + +
15B GLN* 1.3 78.1 - - - +
17B ARG* 1.3 58.7 + - - +
20B LYS* 3.4 3.1 + - - -
21B ILE* 3.1 61.4 + - + +
23B ALA* 4.5 9.4 - - + -
36B ARG* 5.7 0.2 - - - +
37B VAL* 4.1 21.9 + - + +
64B PHE* 4.0 27.6 - - + -
66B PRO* 3.8 11.9 - - + -
70B VAL* 3.6 20.9 - - + -
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 3.3 12.0 + - - +
14B ASN* 2.3 45.0 + - - +
16B LEU* 1.3 79.1 - - - +
18B LYS* 1.3 86.7 + - - +
20B LYS* 3.6 13.2 + - - +
37B VAL* 3.5 23.6 - - + +
38B VAL* 3.3 28.9 + - - +
39B SER* 4.5 7.0 - - - +
40B PHE* 4.7 8.7 - - - -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 5.4 2.2 - - - -
14B ASN* 2.7 47.0 + - - +
15B GLN* 2.6 35.4 + - - +
17B ARG* 1.3 96.5 - - - +
19B GLU* 1.3 62.8 + - + +
20B LYS* 3.1 11.0 + - - +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 2.9 38.7 + - - +
18B LYS* 1.3 78.5 - - + +
20B LYS* 1.3 70.1 + - - +
21B ILE* 3.1 23.7 + - + +
68B LYS* 5.3 6.6 + - - +
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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