Contacts of the helix formed by residues 31 - 43 (chain B) in PDB entry 1NSH
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 SER 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LEU* 1.3 87.4 - - - +
32B LYS* 1.3 65.5 + - - +
33B THR* 3.2 9.0 + - - -
34B GLU* 2.9 55.5 + - - +
35B PHE* 3.0 13.0 + - - +
70B GLN* 3.4 15.9 - - - +
71B LEU* 3.2 9.3 - - - +
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Residues in contact with LYS 32 (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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31B SER* 1.3 71.6 + - - +
33B THR* 1.3 58.4 + - - +
35B PHE* 3.3 5.7 - - - +
36B LEU* 3.0 20.5 - - - +
60B MET* 3.3 37.3 - - + +
63B LEU* 5.3 0.9 - - + -
65B LEU* 3.7 32.8 - - + +
70B GLN* 4.9 0.4 - - - +
71B LEU* 2.8 26.0 - - + +
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Residues in contact with THR 33 (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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31B SER* 3.1 7.5 + - - +
32B LYS* 1.3 76.8 - - - +
34B GLU* 1.3 66.5 + - - +
35B PHE 2.9 1.6 - - - -
36B LEU* 2.7 44.0 + - + +
37B SER* 3.6 2.8 + - - -
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Residues in contact with GLU 34 (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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20B TYR* 2.7 54.6 - - + +
23B LYS* 6.3 0.7 - - - +
30B LEU* 3.0 32.8 - - + +
31B SER* 2.9 32.6 + - - +
33B THR* 1.3 83.7 - - - +
35B PHE* 1.3 58.0 + - - +
37B SER* 3.0 6.4 + - - -
38B PHE 3.5 1.0 + - - -
70B GLN* 5.2 1.2 - - - +
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Residues in contact with PHE 35 (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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30B LEU* 4.6 4.4 - - + +
31B SER 3.0 7.8 + - - +
32B LYS 3.3 13.7 - - - +
33B THR 2.9 0.2 - - - -
34B GLU* 1.3 77.0 - - - +
36B LEU* 1.3 65.3 + - - +
38B PHE* 3.3 9.9 + + - -
39B MET* 3.0 40.2 + - + +
59B MET* 5.4 1.8 - - + -
60B MET* 4.1 8.7 - - + -
71B LEU* 4.0 13.2 - - + -
76B PHE* 3.0 66.6 - + - -
79B LEU* 3.0 52.3 - - + -
80B ILE* 4.1 4.0 - - + -
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Residues in contact with LEU 36 (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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32B LYS 3.0 25.6 - - - +
33B THR* 2.7 31.6 + - + +
35B PHE* 1.3 73.9 - - - +
37B SER* 1.3 58.7 + - - +
39B MET* 3.3 4.1 + - - +
40B ASN* 2.8 41.3 + - - +
56B LEU* 5.4 14.4 - - + -
60B MET* 4.0 14.1 - - + -
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Residues in contact with SER 37 (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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20B TYR* 2.6 40.6 + - - -
33B THR 4.1 2.0 + - - -
34B GLU* 3.0 5.2 + - - -
36B LEU* 1.3 80.4 - - - +
38B PHE* 1.3 50.7 + - - +
40B ASN* 3.3 6.2 + - - +
41B THR* 2.7 39.5 + - - +
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Residues in contact with PHE 38 (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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6A THR* 3.6 27.4 - - + -
16B VAL* 3.3 39.0 - - + -
19B LYS* 5.0 6.5 - - + -
20B TYR* 3.3 36.9 + + + -
34B GLU 3.5 3.8 + - - +
35B PHE* 3.3 15.2 + + + +
36B LEU 3.2 0.4 - - - -
37B SER* 1.3 81.9 + - - +
39B MET* 1.3 58.4 + - - +
41B THR* 3.2 6.0 - - - +
42B GLU* 2.6 65.5 + - + +
43B LEU* 4.4 6.5 - - + -
76B PHE* 3.4 29.2 - + + -
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Residues in contact with MET 39 (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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35B PHE* 3.0 28.4 + - + +
36B LEU 3.6 7.9 - - - +
38B PHE* 1.3 78.0 - - - +
40B ASN* 1.3 56.3 + - - +
43B LEU* 2.7 81.3 + - + +
46B PHE* 4.7 5.4 - - + -
47B THR* 3.2 23.6 - - + -
56B LEU* 3.2 33.9 - - + -
59B MET* 4.5 2.9 - - - -
80B ILE* 4.8 0.2 - - + -
83B LEU* 3.1 33.0 - - + -
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Residues in contact with ASN 40 (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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36B LEU* 2.8 40.8 + - - +
37B SER* 4.0 5.5 - - - +
39B MET* 1.3 77.7 - - - +
41B THR* 1.3 57.7 + - - +
43B LEU 4.6 0.9 - - - -
44B ALA* 4.4 13.4 - - - +
47B THR* 3.6 29.1 + - - +
56B LEU* 5.6 2.1 - - - +
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Residues in contact with THR 41 (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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20B TYR* 4.0 9.9 - - + +
37B SER* 2.7 30.4 + - - +
38B PHE* 3.2 10.1 - - - +
40B ASN* 1.3 76.3 - - - +
42B GLU* 1.3 85.3 + - + +
43B LEU 3.7 0.9 - - - -
44B ALA* 5.3 1.3 - - - -
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Residues in contact with GLU 42 (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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1A SER* 5.2 4.9 - - - -
4A THR* 3.9 14.4 + - - +
5A GLU* 5.8 2.9 - - - +
6A THR* 3.1 25.0 + - - +
19B LYS* 4.5 15.1 + - - +
20B TYR* 5.3 1.6 - - - -
38B PHE* 2.6 49.3 + - + +
41B THR* 1.3 98.8 + - + +
43B LEU* 1.3 74.3 + - - +
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Residues in contact with LEU 43 (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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1A SER* 5.0 2.7 + - - -
6A THR* 3.5 14.6 - - + -
7A GLU* 4.7 6.3 - - + +
10A ILE* 3.3 29.4 - - + -
35B PHE* 5.7 0.2 - - + -
38B PHE* 4.4 8.5 - - + -
39B MET* 2.7 51.3 + - + +
42B GLU* 1.3 88.4 - - - +
44B ALA* 1.3 64.8 + - - +
45B ALA* 3.2 3.8 - - + +
46B PHE* 3.4 26.1 + - + +
47B THR* 3.2 14.6 + - - +
80B ILE* 3.4 26.5 - - + -
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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