Contacts of the strand formed by residues 34 - 42 (chain A) in PDB entry 5NS3
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 LEU 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 5.4 0.4 - - + -
33A ARG* 1.3 82.7 - - - +
35A GLU* 1.3 59.6 + - - +
36A LYS 5.7 0.4 - - - +
99A MET* 3.7 27.3 - - + +
100A TRP* 3.7 35.6 - - + -
103A LEU* 3.3 33.7 - - + -
159A VAL* 3.9 10.8 - - + -
160A VAL 3.9 4.3 - - - +
161A THR* 3.9 15.3 - - + +
172A LEU* 4.1 7.9 - - + +
173A LEU* 3.7 29.6 - - + -
176A LEU* 4.1 9.4 - - + -
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Residues in contact with GLU 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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33A ARG* 3.4 1.6 + - - -
34A LEU* 1.3 74.1 - - - +
36A LYS* 1.3 77.4 + - + +
95A ARG* 4.2 22.9 + - - +
96A ARG 4.9 0.5 + - - -
99A MET* 3.8 8.6 - - - +
160A VAL* 2.9 38.1 + - + +
161A THR 4.6 2.9 - - - +
162A THR* 4.1 25.2 - - + +
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Residues in contact with LYS 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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34A LEU* 5.7 0.3 - - - +
35A GLU* 1.3 95.2 + - - +
37A VAL* 1.3 66.6 + - - +
38A VAL* 4.0 13.9 - - + +
93A THR* 3.8 17.1 - - + +
94A LEU 3.2 13.9 - - - +
95A ARG* 3.7 32.4 - - + +
99A MET* 3.6 4.6 - - - +
158A ALA 3.8 0.2 - - - +
159A VAL* 4.8 0.3 - - - +
160A VAL* 2.9 49.8 + - + +
29C A 4.3 1.4 + - - -
30C C 2.8 28.6 + - - -
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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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34A LEU* 5.4 0.4 - - + -
36A LYS* 1.3 80.5 - - - +
38A VAL* 1.3 61.9 + - - +
39A ILE* 4.3 5.4 - - + -
92A VAL 3.8 1.4 - - - +
94A LEU* 2.9 39.0 + - + +
99A MET* 3.6 24.0 - - + +
102A PHE* 4.1 20.6 - - + -
103A LEU* 4.3 21.1 - - + -
157A ILE* 3.7 27.6 - - + -
158A ALA 3.2 4.0 - - - +
159A VAL* 4.3 17.3 - - + -
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Residues in contact with VAL 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 LYS* 4.0 33.9 - - + +
37A VAL* 1.3 76.1 - - - +
39A ILE* 1.3 64.7 + - - +
40A ASN 4.1 0.2 - - - -
91A ARG* 4.1 21.5 - - + +
92A VAL 3.4 9.2 - - - +
93A THR* 4.1 13.9 - - + +
156A ASP 3.6 1.2 - - - +
157A ILE* 3.3 4.7 - - - +
158A ALA* 2.8 41.5 + - + +
160A VAL* 5.0 0.7 - - + -
28C C 4.5 4.3 + - - +
29C A 3.8 34.3 - - - +
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Residues in contact with ILE 39 (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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37A VAL* 4.3 10.3 - - + -
38A VAL* 1.3 75.4 - - - +
40A ASN* 1.3 64.8 + - - +
60A LEU* 4.0 14.5 - - + +
64A THR* 3.9 17.3 - - + -
90A LEU 3.9 0.3 - - - +
91A ARG* 3.2 7.0 - - - +
92A VAL* 2.8 42.8 + - + +
94A LEU* 4.0 9.4 - - + -
102A PHE* 3.2 43.5 - - + -
155A MET* 3.2 36.1 - - + -
156A ASP 3.5 3.1 - - - +
157A ILE* 4.4 4.9 - - + -
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Residues in contact with ASN 40 (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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38A VAL 4.1 0.8 - - - -
39A ILE* 1.3 77.2 - - - +
41A GLN* 1.3 60.3 + - - +
42A GLY* 3.8 11.3 + - - -
71A THR* 4.2 11.1 + - - +
89A GLY* 5.0 2.1 - - - -
90A LEU 3.3 15.5 + - - +
91A ARG* 3.6 25.2 - - + +
154A GLY 3.8 0.5 - - - +
155A MET* 3.6 2.4 - - - -
156A ASP* 2.9 41.2 + - + +
27C G 3.6 12.6 + - - -
28C C 3.6 46.0 + - - +
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Residues in contact with GLN 41 (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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39A ILE 4.2 0.6 - - - -
40A ASN* 1.3 70.5 - - - +
42A GLY* 1.3 73.8 + - - +
43A LEU* 4.1 7.3 - - + +
56A ALA* 5.5 6.2 + - + +
60A LEU* 4.2 34.3 - - + +
89A GLY* 3.3 2.1 - - - -
90A LEU* 2.7 48.0 + - + +
154A GLY 3.9 10.9 + - - +
155A MET* 3.9 26.8 - - + +
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Residues in contact with GLY 42 (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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40A ASN* 3.8 10.1 + - - -
41A GLN* 1.3 84.7 - - - +
43A LEU* 1.3 67.2 + - - +
88A ILE 3.9 7.2 - - - -
154A GLY 3.1 28.1 + - - +
27C G 5.5 3.6 - - - -
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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