Contacts of the strand formed by residues 111 - 120 (chain B) in PDB entry 2NU5
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.8 20.4 - - + -
29B LEU* 2.9 31.8 + - + +
30B ASP 3.6 1.4 + - - -
31B ALA* 4.6 6.3 - - - +
32B ILE* 3.9 28.3 - - + -
39B HIS 4.7 1.6 - - - +
68B TYR* 3.6 4.5 - - - +
69B ILE* 2.9 49.2 + - + +
106B SER 3.7 15.5 - - - +
107B ALA* 4.2 5.8 - - + -
110B TYR* 1.3 75.7 - - - +
112B ASP* 1.3 57.7 + - - +
113B SER 3.7 10.5 - - - +
114B LEU* 3.9 22.7 - - + -
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Residues in contact with ASP 112 (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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8A GLY* 3.4 5.2 - - - -
9A GLY 3.0 22.5 + - - +
11A GLY* 3.2 39.0 + - - +
12A GLY* 3.5 1.6 - - - -
67B ASP 3.4 5.7 - - - +
68B TYR* 3.4 22.4 - - - +
69B ILE 4.2 0.9 - - - -
106B SER* 3.0 9.2 + - - +
107B ALA* 3.5 3.1 - - - -
108B GLY 3.1 13.7 + - - -
111B LEU* 1.3 74.3 - - - +
113B SER* 1.3 60.2 + - - +
122B NAG 2.5 50.0 + - - -
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Residues in contact with SER 113 (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 LYS* 3.4 31.0 + - - -
7A PHE 3.1 14.6 - - - -
9A GLY 3.5 6.8 + - - -
69B ILE* 4.1 4.7 - - - -
105B GLY* 3.2 4.7 - - - -
106B SER* 3.0 45.9 + - - +
111B LEU* 3.5 10.7 - - - +
112B ASP* 1.3 80.6 - - - +
114B LEU* 1.3 63.8 - - - +
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Residues in contact with LEU 114 (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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5A ARG 3.8 1.0 - - - +
6A LYS* 3.2 7.3 - - - +
7A PHE* 2.8 36.6 + - + +
15A PHE* 4.4 4.7 - - + -
32B ILE* 4.3 7.2 - - + -
63B ILE* 4.0 20.9 - - + -
69B ILE* 4.0 23.3 - - + +
72B ILE* 4.3 18.2 - - + -
103B ILE* 3.6 18.2 - - + -
104B ASN 3.5 13.7 - - - +
105B GLY* 4.0 0.7 - - - -
111B LEU* 3.9 27.8 - - + -
113B SER* 1.3 81.4 - - - +
115B ASP* 1.3 58.2 + - - +
116B ILE* 3.9 15.3 - - + -
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Residues in contact with ASP 115 (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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4A HIS* 3.0 28.3 + - - -
5A ARG 3.5 9.8 - - - +
6A LYS* 4.2 9.7 + - + +
103B ILE* 3.8 0.3 - - - -
104B ASN* 2.8 47.8 + - + +
105B GLY* 4.0 2.2 - - - +
114B LEU* 1.3 71.7 - - - +
116B ILE* 1.3 62.5 + - - +
117B TYR* 2.9 34.3 + - - -
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Residues in contact with ILE 116 (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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4A HIS* 3.1 4.9 - - - -
5A ARG 2.9 31.8 + - - +
7A PHE* 3.7 28.9 - - + -
61B MET* 4.0 16.4 - - + -
63B ILE* 4.1 11.0 - - + -
72B ILE* 5.8 0.2 - - + -
95B LEU* 3.9 22.9 - - + -
100B VAL* 4.1 17.9 - - + -
102B GLN 3.6 1.8 - - - -
103B ILE* 3.8 33.7 - - + -
114B LEU* 4.0 15.0 - - + -
115B ASP* 1.3 71.7 + - - +
117B TYR* 1.3 61.4 + - - +
118B TYR* 3.5 8.9 - - + -
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Residues in contact with TYR 117 (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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2A LEU* 4.0 21.1 - - + -
3A THR 3.2 7.9 - - - +
4A HIS* 3.5 28.4 + + + -
99A LYS* 5.6 2.8 + - - -
101A ILE* 3.8 39.6 - - + +
2B LEU* 4.1 16.6 - - + -
100B VAL* 3.7 2.6 - - - +
101B ILE* 2.8 29.7 + - + -
102B GLN* 2.9 29.2 + - + +
104B ASN* 3.7 18.7 + - - -
115B ASP* 2.9 42.7 + - - -
116B ILE* 1.3 71.8 - - - +
118B TYR* 1.3 58.7 + - - +
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Residues in contact with TYR 118 (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 3.6 0.5 - - - +
2A LEU* 3.7 5.5 - - - +
3A THR* 2.9 62.5 + - + +
4A HIS 4.1 0.2 - - - -
5A ARG* 3.4 36.8 - - + +
95B LEU* 3.6 29.4 - - + +
98B VAL* 3.6 21.5 - - + -
99B LYS 3.2 15.9 - - - +
100B VAL* 3.8 13.9 - - + -
101B ILE* 4.0 2.7 - - - +
116B ILE* 3.5 21.8 - - + -
117B TYR* 1.3 76.4 - - - +
119B GLU* 1.3 67.3 + - - +
120B GLN* 3.6 25.2 + - + -
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Residues in contact with GLU 119 (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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0A ACE 3.8 24.9 - - + +
1A SER 3.5 15.5 - - - +
2A LEU* 4.9 0.9 - - - -
117A TYR* 2.9 33.4 + - + -
4B HIS* 4.1 5.2 + - - -
98B VAL* 3.1 8.1 - - - +
99B LYS* 2.9 37.9 + - - +
101B ILE* 4.2 16.2 - - + -
118B TYR* 1.3 76.1 - - - +
120B GLN* 1.3 59.7 + - - +
121B TYR* 2.7 45.1 + - + -
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Residues in contact with GLN 120 (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 4.1 8.7 + - - -
3A THR* 4.7 6.6 - - + +
95B LEU* 5.1 2.8 - - - +
96B SER 2.9 27.9 + - - +
97B ASN* 3.1 8.7 + - - +
98B VAL* 3.5 13.1 - - - +
118B TYR* 3.6 21.8 + - + -
119B GLU* 1.3 71.2 - - - +
121B TYR* 1.3 86.7 + - - +
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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