Contacts of the helix formed by residues 51 - 65 (chain B) in PDB entry 3NSI
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 ARG 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B PRO* 4.2 2.0 - - - -
48B THR* 3.3 19.2 + - - +
49B GLU 3.3 1.2 - - - -
50B PHE* 1.3 87.8 + - + +
52B GLU* 1.3 60.0 + - - +
53B CYS 3.4 2.7 - - - -
54B ASP* 3.8 8.8 + - - -
55B TYR* 2.9 30.5 + - - +
84B LEU* 2.6 47.6 + - - +
85B TYR* 3.6 35.2 - - + +
90B PHE* 3.2 22.4 + - - +
91B LYS 3.9 9.1 + - - +
93B CYS* 2.3 42.0 + - - +
95B SER 4.3 9.8 + - - -
96B GLU* 5.6 0.4 - - - +
97B PRO* 4.3 14.3 - - - +
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Residues in contact with GLU 52 (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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47B PRO* 4.0 26.4 - - + +
48B THR 3.5 10.0 + - - +
49B GLU* 3.5 18.8 - - - +
50B PHE 3.6 1.8 - - - -
51B ARG* 1.3 78.5 - - - +
53B CYS* 1.3 64.9 + - - +
55B TYR* 3.4 2.3 + - - +
56B ASN* 3.1 38.0 + - - +
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Residues in contact with CYS 53 (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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50B PHE 5.4 0.6 + - - -
51B ARG 3.4 0.2 - - - -
52B GLU* 1.3 77.7 - - - +
54B ASP* 1.3 72.8 + - - +
56B ASN* 3.3 10.7 + - - +
57B LYS* 3.1 44.0 + - - +
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Residues in contact with ASP 54 (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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50B PHE 4.1 11.7 - - - +
51B ARG* 3.9 12.1 - - - +
52B GLU 3.4 0.4 - - - -
53B CYS* 1.3 82.8 - - - +
55B TYR* 1.3 61.7 + - - +
57B LYS* 3.5 11.5 + - - +
58B PHE* 3.1 23.6 + - - +
85B TYR* 3.5 26.7 + - + +
96B GLU* 5.0 4.3 - - - +
97B PRO* 3.5 24.6 - - + +
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP 4.0 11.6 + - - -
46B THR* 5.2 0.2 - - - -
47B PRO* 3.6 30.7 - - + -
51B ARG 2.9 20.3 + - - +
52B GLU 3.5 3.8 - - - +
54B ASP* 1.3 77.7 - - - +
56B ASN* 1.3 70.2 + - - +
58B PHE* 3.2 4.7 + + - +
59B MET* 3.0 61.9 + - + +
82B LEU* 4.7 12.2 - - + +
85B TYR* 4.0 23.5 - + + -
86B CYS* 3.8 29.2 - - - -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO* 5.4 1.2 - - - +
52B GLU* 3.1 27.3 + - - +
53B CYS* 3.3 9.6 + - - +
55B TYR* 1.3 91.8 - - - +
57B LYS* 1.3 57.7 + - + +
59B MET* 3.3 5.0 + - - +
60B SER* 2.9 30.9 + - - -
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Residues in contact with LYS 57 (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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53B CYS* 3.1 32.2 + - - +
54B ASP* 3.8 9.6 + - - +
56B ASN* 1.3 75.8 - - + +
58B PHE* 1.3 62.3 + - - +
60B SER* 2.8 21.8 + - - -
61B VAL* 3.0 20.5 + - + +
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Residues in contact with PHE 58 (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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34B LEU* 5.7 0.2 - - + -
38B LEU* 4.1 1.6 - - + -
54B ASP 3.1 14.3 + - - +
55B TYR 3.4 8.3 - - - +
57B LYS* 1.3 79.3 - - - +
59B MET* 1.3 73.9 + - + +
61B VAL* 3.4 15.9 + - + +
62B LEU* 3.4 40.8 + - + +
77B ARG* 6.1 1.3 - - - -
78B SER* 3.8 31.0 - - - -
81B CYS* 4.2 15.7 - - + -
82B LEU* 3.2 32.3 - - + -
85B TYR* 3.7 24.9 - + + +
99B CYS 5.1 7.2 - - - -
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Residues in contact with MET 59 (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 LYS* 4.2 13.9 - - + +
38B LEU* 4.8 10.3 - - + -
39B GLN* 3.5 42.4 - - + +
55B TYR* 3.0 54.6 + - + +
56B ASN* 4.0 5.4 - - - +
58B PHE* 1.3 95.9 - - + +
60B SER* 1.3 63.7 + - - +
62B LEU* 3.4 13.7 + - + +
63B ASP* 3.3 24.4 + - - +
82B LEU* 4.9 3.6 - - - -
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Residues in contact with SER 60 (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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56B ASN 2.9 16.0 + - - -
57B LYS* 2.8 24.4 + - - -
59B MET* 1.3 73.4 - - - +
61B VAL* 1.3 56.4 + - - +
63B ASP* 2.9 12.7 + - - +
64B THR* 2.7 36.7 + - - +
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Residues in contact with VAL 61 (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 GLN* 5.7 2.7 - - - +
57B LYS* 3.0 19.3 + - + +
58B PHE* 3.5 11.9 - - + +
60B SER* 1.3 83.9 + - - +
62B LEU* 1.3 62.0 + - + +
64B THR* 3.4 11.7 - - + -
65B ASN* 2.9 38.8 + - + +
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Residues in contact with LEU 62 (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 GLN* 2.8 47.4 - - - +
32B ALA* 4.5 2.6 + - - -
34B LEU* 4.0 14.8 - - + -
35B LYS* 4.0 27.2 - - + +
38B LEU* 3.7 29.6 - - + -
58B PHE* 3.4 34.0 + - + +
59B MET* 3.7 15.7 - - - +
60B SER 3.2 0.4 - - - -
61B VAL* 1.3 81.7 - - + +
63B ASP* 1.3 63.4 + - - +
65B ASN 3.3 12.0 - - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 2.9 38.0 + - - +
39B GLN* 5.3 2.4 + - - -
59B MET 3.3 11.5 + - - +
60B SER* 2.9 13.4 + - - +
62B LEU* 1.3 80.2 - - - +
64B THR* 1.3 68.2 + - - +
65B ASN 3.6 2.6 - - - +
66B LYS* 5.3 1.6 - - - +
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Residues in contact with THR 64 (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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60B SER 2.7 13.5 + - - +
61B VAL* 3.0 33.2 - - + +
63B ASP* 1.3 73.8 - - - +
65B ASN* 1.3 81.3 + - + +
66B LYS* 3.3 7.8 + - - +
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Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.4 27.3 - - + +
32B ALA 5.0 0.3 + - - -
61B VAL* 2.9 23.5 + - + +
62B LEU 3.3 18.0 - - - +
63B ASP 3.6 2.1 - - - +
64B THR* 1.3 85.3 + - + +
66B LYS* 1.3 59.4 + - - +
67B ASP* 3.7 4.9 - - + +
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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