Contacts of the helix formed by residues 31 - 44 (chain J) in PDB entry 3NM9
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 LYS 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29J GLY 3.8 4.7 + - - +
30J ILE* 1.3 75.7 - - - +
32J VAL* 1.3 56.2 + - - +
33J THR* 2.8 29.8 + - - +
34J GLU* 2.6 36.9 + - + +
35J VAL* 2.8 10.9 + - - -
7L A 3.3 28.6 + - - +
8L T 4.8 14.0 + - - +
4P LYS* 5.7 7.5 - - - +
7P ARG* 5.9 2.8 - - - +
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Residues in contact with VAL 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ARG* 4.9 11.0 - - - +
31J LYS* 1.3 71.1 - - - +
33J THR* 1.3 57.2 + - - +
35J VAL* 3.8 10.9 - - - +
36J ALA* 2.9 31.6 + - + +
8K T 5.2 7.6 - - - +
9K C 5.0 7.7 - - - +
4L G 5.3 1.1 - - - +
5L A 3.4 50.3 - - + +
6L T 3.7 29.2 - - - +
7L A 3.8 6.7 + - - +
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Residues in contact with THR 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LYS* 2.8 34.5 + - - +
32J VAL* 1.3 75.7 + - - +
34J GLU* 1.3 57.2 + - - -
36J ALA* 4.0 2.4 - - - +
37J LYS* 3.3 26.5 + - - +
8K T 4.0 11.5 + - - +
9K C 3.4 53.7 - - - +
7L A 5.2 8.0 - - - -
7P ARG* 5.9 1.7 + - - +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ASN* 5.7 1.2 + - - -
30J ILE* 3.5 25.3 - - + +
31J LYS* 2.6 23.7 + - + +
33J THR* 1.3 73.9 - - - +
35J VAL* 1.3 54.5 + - - +
37J LYS* 3.3 29.2 - - - +
38J ARG* 2.8 39.5 + - - +
41J GLU* 5.1 0.5 - - - +
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Residues in contact with VAL 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LEU* 5.2 4.9 - - + -
20J ARG* 3.9 35.4 - - + +
23J ILE* 4.6 18.5 - - + +
24J LYS* 4.4 14.4 - - + -
30J ILE* 3.5 36.5 - - + +
31J LYS 2.8 13.9 + - - +
32J VAL* 3.7 12.3 - - + +
34J GLU* 1.3 72.0 - - - +
36J ALA* 1.3 58.3 + - - +
38J ARG* 2.9 5.5 + - - +
39J GLY* 2.7 33.6 + - - -
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Residues in contact with ALA 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 3.4 13.1 + - - +
16J LEU* 5.2 4.9 - - + -
20J ARG* 6.1 0.7 - - - +
32J VAL* 2.9 23.1 + - + +
33J THR 4.0 0.7 - - - +
35J VAL* 1.3 73.4 - - + +
37J LYS* 1.3 63.6 + - - +
39J GLY 3.3 7.3 + - - -
40J GLY 3.4 5.9 + - - -
9K C 3.9 26.2 - - - +
10K G 3.3 32.0 - - - +
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Residues in contact with LYS 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J THR* 3.3 13.7 + - - +
34J GLU* 3.3 26.0 - - - +
35J VAL 3.2 0.6 - - - -
36J ALA* 1.3 80.9 - - - +
38J ARG* 1.3 60.7 + - - +
40J GLY* 3.3 7.6 + - - -
41J GLU* 3.1 35.3 + - - +
44J ARG* 4.3 4.0 + - - +
9K C 4.6 2.2 + - - -
10K G 2.8 43.0 + - - +
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Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ILE* 3.8 27.4 - - + +
26J GLU* 4.0 15.6 + - - -
27J ASN* 4.8 13.4 + - - +
30J ILE* 4.5 1.8 - - + -
34J GLU* 2.8 32.1 + - - +
35J VAL 3.5 3.6 - - - +
37J LYS* 1.3 70.5 - - - +
39J GLY* 1.3 68.5 + - - +
41J GLU* 3.3 32.0 + - - +
42J LEU* 3.2 51.1 + - + +
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Residues in contact with GLY 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J TYR* 3.8 7.4 - - - -
15J TRP* 3.6 5.9 - - - -
16J LEU* 3.8 23.1 - - - -
23J ILE* 4.5 7.6 - - - +
35J VAL 2.7 18.8 + - - -
36J ALA 3.3 3.8 + - - -
37J LYS 3.2 0.4 - - - -
38J ARG* 1.3 70.9 - - - +
40J GLY* 1.3 62.7 + - - +
42J LEU* 3.1 5.3 + - - +
43J TRP* 2.8 23.4 + - - +
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Residues in contact with GLY 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J TYR* 3.7 10.5 - - - -
36J ALA 3.4 6.3 + - - -
37J LYS 3.3 8.8 + - - -
39J GLY* 1.3 71.6 - - - +
41J GLU* 1.3 51.5 + - - +
42J LEU 2.6 13.0 + - - -
43J TRP* 2.8 4.5 + - - -
44J ARG* 2.8 46.6 + - - +
10K G 4.1 13.7 - - - -
11K C 4.2 2.7 - - - -
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Residues in contact with GLU 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J GLU* 5.1 0.9 - - - +
37J LYS* 3.1 42.4 - - - +
38J ARG* 3.7 30.3 + - - +
40J GLY* 1.3 70.6 - - - +
42J LEU* 1.3 55.5 + - - +
44J ARG* 3.4 22.4 + - - +
45J ALA* 3.6 17.8 - - - +
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J TRP* 3.9 22.1 - - + -
19J ALA* 6.0 0.9 - - + -
22J SER* 6.2 0.4 - - - +
23J ILE* 4.3 23.1 - - + -
26J GLU* 5.0 6.5 - - - +
38J ARG* 3.2 46.0 + - - +
39J GLY 3.1 3.3 + - - +
40J GLY 2.6 6.5 + - - -
41J GLU* 1.3 75.0 - - - +
43J TRP* 1.3 61.5 + - - +
45J ALA* 3.6 6.9 - - + +
46J MET* 3.5 20.5 + - + +
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Residues in contact with TRP 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ALA* 3.9 25.1 - - + -
12J TYR* 3.6 40.8 - + + +
15J TRP* 3.6 52.3 - + + -
39J GLY 2.8 14.7 + - - +
40J GLY 2.8 2.8 + - - +
42J LEU* 1.3 73.0 - - - +
44J ARG* 1.3 60.6 + - + +
45J ALA 2.3 20.1 + - - -
46J MET* 2.6 22.5 + - - +
49J LYS* 3.5 54.4 + - + +
52J TRP* 4.1 17.5 - + + -
53J GLU* 5.1 2.9 - - + -
11K C 5.0 10.3 + - - -
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Residues in contact with ARG 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ARG* 5.0 2.0 - - - -
37J LYS* 4.3 3.8 + - - +
40J GLY* 2.8 20.8 + - - +
41J GLU* 3.4 37.4 - - - +
43J TRP* 1.3 74.9 - - + +
45J ALA* 1.3 60.2 + - - +
49J LYS* 5.1 3.4 - - - +
10K G 4.3 8.3 + - - -
11K C 3.3 36.3 + - - +
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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