Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 3NSH
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 GLN 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A THR* 2.9 4.6 - - - -
26A VAL* 2.8 47.5 + - + +
29A PRO* 3.9 7.7 + - + +
30A PRO* 1.3 75.1 - - - +
32A THR* 1.3 64.4 + - - +
33A LEU* 3.7 6.2 + - + +
57A TYR 3.9 5.0 - - - +
58A TYR* 3.7 16.5 - - - -
59A GLN* 2.9 54.1 + - - +
62A LEU* 4.1 14.4 + - - +
63A SER* 4.1 15.4 - - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.9 33.9 + - + +
24A MET 3.4 4.9 - - - -
25A THR* 3.7 13.5 - - - +
30A PRO* 4.1 2.8 + - - +
31A GLN* 1.3 71.7 - - - +
33A LEU* 1.3 66.5 + - - +
56A ARG* 3.0 50.2 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.7 0.5 - - - -
24A MET* 2.8 38.0 + - + +
25A THR* 5.9 0.2 - - - -
26A VAL* 4.1 19.3 - - + -
31A GLN* 3.7 7.8 + - + +
32A THR* 1.3 84.6 - - - +
34A ASN* 1.3 61.1 + - - +
35A ILE* 3.8 16.2 + - + +
46A VAL* 3.9 30.7 - - + -
56A ARG* 4.1 10.8 - - + +
57A TYR* 4.1 22.4 - - - -
58A TYR* 4.1 19.1 - - + +
122A GLU* 3.5 26.7 - - + +
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Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.1 33.4 - - + -
22A VAL 3.7 2.9 - - - -
23A GLU* 4.1 18.2 - - - +
33A LEU* 1.3 71.8 - - - +
35A ILE* 1.3 61.6 + - - +
56A ARG* 3.6 16.3 + - - +
120A ASN* 2.7 46.3 + - - +
121A TRP* 3.4 4.5 - - - +
122A GLU* 2.8 36.4 + - - +
123A GLY 3.4 4.9 + - - -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.1 3.6 - - - +
22A VAL* 2.8 40.2 + - - +
24A MET* 3.5 34.1 - - + -
33A LEU* 3.9 20.2 - - + +
34A ASN* 1.3 81.7 - - - +
36A LEU* 1.3 62.3 + - - +
44A PHE* 3.9 5.6 - - + -
46A VAL* 3.6 31.6 - - + -
123A GLY* 3.5 9.9 - - - +
124A ILE* 3.4 7.9 - - - +
125A LEU* 3.4 39.9 - - + +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 4.1 0.2 - - - +
19A GLY* 4.1 16.2 - - - -
20A TYR 3.3 15.9 - - - +
21A TYR* 3.9 3.7 - - - +
34A ASN 4.2 0.4 + - - -
35A ILE* 1.3 70.5 - - - +
37A VAL* 1.3 78.4 + - - +
38A ASP* 3.6 16.8 - - + -
121A TRP* 3.9 31.5 - - + +
123A GLY 2.8 17.3 + - - +
124A ILE* 3.4 12.9 - - + -
125A LEU* 2.7 34.0 + - - +
235A SER 5.2 0.7 - - - +
236A GLY* 4.5 10.1 - - - +
407A 957 3.8 32.3 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.2 10.1 - - + -
20A TYR* 2.9 22.4 + - + +
22A VAL* 3.6 34.5 - - + +
35A ILE 3.7 3.8 - - - +
36A LEU* 1.3 78.6 - - - +
38A ASP* 1.3 54.8 + - - +
125A LEU* 4.1 7.4 - - + -
127A LEU* 3.8 18.2 - - + -
158A LEU* 3.9 31.6 - - + -
160A LEU* 6.0 1.1 - - + -
180A MET* 4.0 14.1 - - + -
235A SER* 2.8 26.0 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.6 13.0 - - + -
37A VAL* 1.3 75.5 - - - +
39A THR* 1.3 61.1 - - - +
40A GLY* 2.9 19.0 + - - -
41A SER* 2.6 26.9 + - - +
124A ILE* 3.4 15.2 - - + +
125A LEU 3.0 15.6 + - - +
127A LEU* 2.7 26.6 + - - +
234A ASP* 3.2 12.1 - - - +
235A SER* 3.6 1.1 - - - -
236A GLY* 3.4 6.9 - - - +
407A 957 2.8 26.1 + - - -
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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