Contacts of the helix formed by residues 31 - 45 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P GLY 3.3 5.8 + - - +
30P ILE* 1.3 78.3 - - - +
32P VAL* 1.3 71.7 + - + +
33P THR* 3.4 19.8 + - - +
34P GLU* 3.3 53.2 + - + +
35P VAL* 3.3 14.1 + - - +
37P LYS* 5.1 7.5 - - - +
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Residues in contact with VAL 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L C 3.5 47.0 - - + +
20P ARG* 5.5 2.1 + - - -
31P LYS* 1.3 77.0 - - + +
33P THR* 1.3 63.2 + - - +
35P VAL* 3.6 17.5 + - - +
36P ALA* 3.8 5.9 + - - +
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Residues in contact with THR 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K C 4.8 28.7 - - - +
4K G 5.3 4.2 - - - +
31P LYS* 3.4 19.8 + - - +
32P VAL* 1.3 77.0 - - - +
34P GLU* 1.3 61.8 + - - +
36P ALA* 3.2 9.5 + - + +
37P LYS* 3.0 29.6 + - + +
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Residues in contact with GLU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ASN* 4.9 6.1 - - - +
30P ILE* 3.3 29.7 - - + +
31P LYS* 3.3 33.0 + - + +
32P VAL 3.4 0.2 - - - -
33P THR* 1.3 75.3 - - - +
35P VAL* 1.3 60.3 + - - +
37P LYS* 3.9 26.5 + - + +
38P ARG* 2.8 32.0 + - + +
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Residues in contact with VAL 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU* 4.6 7.1 - - + +
20P ARG* 3.9 38.4 - - + +
23P ILE* 3.9 19.4 - - + +
24P LYS* 4.5 10.5 - - + -
30P ILE* 3.6 29.8 - - + +
31P LYS 3.3 17.9 - - - +
32P VAL* 3.7 9.4 - - - +
33P THR 3.1 0.6 - - - -
34P GLU* 1.3 74.2 - - - +
36P ALA* 1.3 55.3 + - - +
38P ARG* 3.3 0.7 + - - +
39P GLY* 2.6 35.3 + - - -
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Residues in contact with ALA 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K C 5.7 3.4 - - - +
4K G 4.2 24.6 - - - +
5K A 5.1 0.7 - - - +
10L G 6.1 2.5 - - - +
12P TYR* 3.6 16.8 + - - +
16P LEU* 5.1 6.3 - - + -
20P ARG* 5.4 1.9 - - - +
32P VAL 3.8 5.6 + - - +
33P THR* 3.2 12.7 + - + +
35P VAL* 1.3 78.1 - - - +
37P LYS* 1.3 53.0 + - - +
39P GLY 3.1 1.2 + - - -
40P GLY* 2.5 36.2 + - - -
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Residues in contact with LYS 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K G 4.5 17.0 - - - +
5K A 5.8 1.6 - - - -
31P LYS* 5.1 7.2 - - - +
33P THR* 3.0 18.3 + - + +
34P GLU* 3.6 28.2 + - + +
36P ALA* 1.3 73.2 - - - +
38P ARG* 1.3 57.7 + - + +
40P GLY* 3.0 4.8 + - - -
41P GLU* 2.8 52.1 + - + +
44P ARG* 4.1 3.6 + - - +
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Residues in contact with ARG 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ILE* 4.0 19.9 - - + +
26P GLU* 3.8 23.6 + - - +
27P ASN* 3.1 32.1 + - - +
30P ILE* 4.8 4.5 - - + -
34P GLU* 2.8 23.9 + - + +
35P VAL 4.0 1.6 - - - +
37P LYS* 1.3 73.6 - - + +
39P GLY* 1.3 52.0 + - - +
41P GLU* 3.2 18.5 + - - +
42P LEU* 2.7 74.3 + - + +
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Residues in contact with GLY 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P TYR* 3.8 3.8 - - - -
15P TRP* 3.2 31.1 - - - -
16P LEU* 4.0 6.7 - - - -
23P ILE* 4.0 10.0 - - - +
35P VAL 2.6 22.4 + - - -
36P ALA 3.4 1.1 - - - -
38P ARG* 1.3 71.5 - - - +
40P GLY* 1.3 57.3 + - - +
42P LEU 3.3 0.5 + - - -
43P TRP* 2.8 25.8 + - - +
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Residues in contact with GLY 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K A 3.7 27.1 - - - -
12P TYR* 3.9 4.8 - - - -
36P ALA 2.5 18.1 + - - -
37P LYS 3.3 3.8 - - - -
39P GLY* 1.3 71.6 - - - +
41P GLU* 1.3 55.2 + - - +
43P TRP* 3.1 3.6 + - - +
44P ARG* 2.9 43.5 + - - +
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Residues in contact with GLU 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P LYS* 2.8 44.6 + - + +
38P ARG* 3.5 21.0 + - - +
40P GLY* 1.3 70.5 - - - +
42P LEU* 1.3 64.3 + - + +
44P ARG* 3.2 20.6 + - - +
45P ALA* 3.1 25.8 + - - +
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Residues in contact with LEU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P TRP* 3.6 20.4 - - + -
19P ALA* 6.1 0.2 - - + -
23P ILE* 3.7 32.5 - - + -
38P ARG* 2.7 59.4 + - - +
41P GLU* 1.3 74.7 - - + +
43P TRP* 1.3 58.5 + - - +
45P ALA* 3.7 7.4 + - + +
46P MET* 3.1 27.6 + - - +
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Residues in contact with TRP 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K A 3.4 19.2 + - - -
6K T 2.8 29.3 + - - -
11P ALA* 4.1 25.6 - - + -
12P TYR* 3.6 33.6 - + + +
15P TRP* 3.8 29.4 - + + -
39P GLY 2.8 17.8 + - - +
40P GLY 3.3 3.8 - - - +
42P LEU* 1.3 73.8 - - - +
44P ARG* 1.3 61.6 + - + +
45P ALA 3.0 1.6 - - - -
46P MET* 2.7 64.0 + - + +
49P LYS* 3.1 44.8 + - + +
52P TRP* 4.4 5.8 - - + -
53P GLU* 5.3 3.4 - - - -
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Residues in contact with ARG 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K A 3.0 45.9 + - - -
37P LYS* 4.1 4.4 + - - +
40P GLY* 2.9 18.9 + - - +
41P GLU* 3.2 37.6 - - - +
43P TRP* 1.3 78.2 - - + +
45P ALA* 1.3 57.3 + - - +
46P MET 3.4 2.8 + - - +
49P LYS* 4.5 7.8 + - - +
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Residues in contact with ALA 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P GLU 3.1 16.5 + - - +
42P LEU* 3.8 8.5 - - + +
43P TRP 3.0 1.0 - - - -
44P ARG* 1.3 75.8 - - - +
46P MET* 1.3 62.3 + - - +
47P LYS* 3.7 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