Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 1NSX
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 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.2 10.5 - - - +
28B THR* 2.8 47.1 + - + +
30B LEU* 2.9 30.6 + - - +
31B GLY 3.7 5.2 - - - +
32B ALA* 1.3 75.6 - - - +
34B ILE* 1.3 71.6 + - - +
35B VAL* 4.0 0.8 - - - +
54B TYR* 3.4 39.9 - - - +
55B LEU* 5.8 0.8 - - - +
59B ALA* 2.8 29.9 + - - +
61B PRO 2.9 22.8 + - - +
62B GLY 3.3 17.5 - - - +
63B ALA* 3.7 11.0 - - - +
103B HIS 3.0 27.5 + - - -
122B PHE* 5.1 0.2 - - - -
143B HIS* 4.8 0.4 - - - -
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Residues in contact with ILE 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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25B ILE* 3.6 32.3 - - + -
26B SER 3.4 12.3 - - - +
27B PHE* 3.6 13.4 - - + -
33B ARG* 1.3 85.2 - - - +
35B VAL* 1.3 64.1 + - - +
36B ASP 3.8 2.5 - - - +
37B TRP* 4.4 4.3 - - + -
45B ILE* 3.7 22.6 - - + +
46B LEU 5.1 2.1 - - - +
54B TYR* 4.2 2.6 + - - -
62B GLY* 2.9 34.7 + - - +
143B HIS* 4.9 2.0 + - + -
151B TRP* 3.6 42.8 - - + -
171B VAL* 4.0 11.7 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.9 17.5 - - + -
14B LEU* 4.1 8.7 - - + -
26B SER* 2.7 22.6 + - - +
27B PHE 4.0 2.0 - - - -
28B THR* 3.5 44.6 - - + +
33B ARG* 4.5 1.1 - - - -
34B ILE* 1.3 77.3 - - - +
36B ASP* 1.3 65.0 + - + +
45B ILE* 3.8 6.3 - - - +
46B LEU 4.2 0.2 - - - +
47B GLY* 3.6 22.2 + - - -
48B PHE 3.7 21.5 - - - +
54B TYR* 3.8 12.3 - - - +
291B HIS* 6.0 0.3 - - - -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.3 8.7 - - - +
26B SER* 2.6 42.5 + - - +
34B ILE* 3.8 1.0 - - - +
35B VAL* 1.3 86.1 - - + +
37B TRP* 1.3 79.3 + - - +
38B GLN* 3.0 29.9 + - - +
43B HIS* 2.8 30.4 + - - +
45B ILE* 3.5 14.0 - - - +
47B GLY 5.9 0.3 + - - -
291B HIS* 5.3 3.9 + - + -
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Residues in contact with TRP 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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23B VAL* 3.6 23.0 - - + +
24B THR 3.3 17.9 - - - -
25B ILE* 3.7 18.6 - - + -
34B ILE* 4.4 0.9 - - + -
36B ASP* 1.3 81.9 + - - +
38B GLN* 1.3 57.6 + - - +
44B LEU* 2.8 50.4 + - + +
45B ILE* 3.8 18.2 + - + +
145B PHE* 3.6 22.8 - + - -
149B ASN 4.1 3.4 - - - -
151B TRP* 3.7 28.0 - + + -
173B PHE* 3.9 27.1 - + - -
267B ILE* 4.2 8.1 - - + -
334B TYR* 3.7 26.5 - - + -
336B LEU* 3.9 27.3 - - + +
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Residues in contact with GLN 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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22B GLY 4.9 0.7 - - - +
23B VAL* 3.5 10.3 - - - +
24B THR* 3.0 43.1 + - - +
36B ASP* 3.0 27.4 + - - +
37B TRP* 1.3 73.1 - - - +
39B LYS* 1.3 61.8 + - - +
41B GLY* 3.2 31.3 + - - +
42B LYS 3.2 17.3 - - - +
43B HIS* 3.2 23.0 + - - -
44B LEU* 4.4 2.2 - - - -
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Residues in contact with LYS 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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23B VAL* 4.2 20.4 - - + +
38B GLN* 1.3 75.1 - - - +
40B ASP* 1.3 99.2 + - - +
41B GLY 3.2 1.1 - - - -
42B LYS* 2.9 23.4 + - - +
44B LEU* 4.4 20.3 - - + +
265B THR* 5.1 10.5 + - + +
336B LEU* 4.6 17.5 - - + -
338B THR* 4.0 27.2 + - - +
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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