Contacts of the strand formed by residues 98 - 107 (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 VAL 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B TYR* 3.6 9.4 - - - -
58B ILE* 3.4 7.6 - - + +
59B SER* 2.9 40.3 + - - +
60B ASN* 4.4 1.1 - - - +
95B LEU* 4.0 16.2 - - + -
96B SER 3.5 14.1 - - - +
97B ASN* 1.3 83.1 + - - +
99B LYS* 1.3 60.8 + - - +
100B VAL* 4.1 16.2 - - + -
118B TYR* 3.6 21.3 - - + -
119B GLU 3.1 11.7 - - - +
120B GLN* 3.5 24.5 - - - +
121B TYR* 4.1 7.2 - - - -
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Residues in contact with LYS 99 (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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104A ASN* 4.8 9.7 - - - +
115A ASP* 5.9 0.4 + - - -
117A TYR* 4.6 9.7 + - - -
16B SER* 6.2 2.9 - - - -
57B TYR* 3.7 40.7 - - + -
58B ILE 3.4 4.0 - - - -
98B VAL* 1.3 73.1 - - - +
100B VAL* 1.3 64.0 + - - +
101B ILE* 3.4 23.8 + - + +
118B TYR* 3.2 2.7 - - - -
119B GLU* 2.9 37.3 + - + +
121B TYR* 3.4 29.8 + - + +
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Residues in contact with VAL 100 (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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16B SER* 5.4 3.5 + - - -
18B LEU* 4.0 20.7 - - + +
57B TYR* 4.6 7.1 - - - +
58B ILE* 3.1 48.6 + - + +
61B MET* 3.9 16.6 - - + -
95B LEU* 5.0 0.4 - - + -
98B VAL* 4.1 11.4 - - + -
99B LYS* 1.3 77.8 - - - +
101B ILE* 1.3 64.5 + - - +
102B GLN 4.0 15.3 - - - +
103B ILE* 4.1 10.8 - - + -
116B ILE* 4.1 10.1 - - + -
117B TYR 3.7 10.8 - - - +
118B TYR* 3.8 3.4 - - + -
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Residues in contact with ILE 101 (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 16.8 - - + -
101A ILE* 5.3 0.7 - - + -
102A GLN* 2.9 40.9 + - + +
104A ASN* 4.0 8.4 - - - +
117A TYR* 3.7 56.8 - - + +
16B SER* 4.7 3.5 + - - -
18B LEU* 4.0 9.2 - - - +
99B LYS* 3.8 35.2 - - + +
100B VAL* 1.3 80.5 - - - +
102B GLN* 1.3 58.2 + - + +
117B TYR* 2.8 15.0 + - + +
118B TYR* 4.2 3.1 - - - -
119B GLU* 4.2 7.0 - - + +
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Residues in contact with GLN 102 (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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17A GLY* 3.4 15.4 - - - +
18A LEU* 3.4 23.6 - - - +
101A ILE* 2.9 47.1 + - + +
102A GLN* 3.3 26.3 + - + +
18B LEU* 4.5 10.4 - - - +
100B VAL* 3.8 2.0 - - - +
101B ILE* 1.3 79.4 - - - +
103B ILE* 1.3 90.7 + - - +
104B ASN* 3.3 24.0 + - - +
115B ASP 4.6 0.2 - - - -
116B ILE* 3.6 1.4 - - - -
117B TYR* 2.9 35.3 + - + +
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Residues in contact with ILE 103 (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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17A GLY* 3.2 23.9 + - - -
18B LEU* 4.1 14.0 - - + +
21B ILE* 3.7 32.5 - - + -
32B ILE* 4.3 10.1 - - + -
34B ILE* 3.4 24.2 - - + +
58B ILE* 4.5 9.0 - - + -
61B MET* 5.3 4.7 - - - -
72B ILE* 5.7 3.6 - - + -
100B VAL* 4.1 8.3 - - + -
102B GLN* 1.3 86.1 + - - +
104B ASN* 1.3 62.4 - - - +
114B LEU* 3.6 29.6 - - + -
115B ASP 3.8 2.9 - - - -
116B ILE* 3.8 20.2 - - + -
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Residues in contact with ASN 104 (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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15A PHE* 3.4 17.3 - - - +
16A SER* 3.4 17.9 + - - +
17A GLY 2.9 21.0 + - - +
99A LYS* 6.2 0.6 - - - +
101A ILE* 4.1 16.2 + - - +
102B GLN* 3.3 15.9 - - - +
103B ILE* 1.3 74.1 - - - +
105B GLY* 1.3 60.7 + - - +
114B LEU* 3.5 12.3 - - - +
115B ASP* 2.8 39.9 + - + +
117B TYR* 3.7 20.1 + - - -
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Residues in contact with GLY 105 (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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14A PRO* 3.4 6.1 - - - +
15A PHE* 2.8 43.6 + - - +
104B ASN* 1.3 81.7 - - - +
106B SER* 1.3 58.3 + - - -
113B SER* 3.2 17.0 - - - -
114B LEU* 4.0 1.8 - - - -
115B ASP* 4.0 4.9 - - - +
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Residues in contact with SER 106 (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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9A GLY 5.8 0.2 - - - -
10A SER 5.3 0.6 + - - -
11A GLY 2.8 23.9 + - - -
12A GLY 3.0 17.8 + - - -
13A SER 3.2 12.0 + - - -
14A PRO* 3.7 4.2 - - - +
15A PHE* 3.4 2.2 - - - -
105B GLY* 1.3 76.1 - - - -
107B ALA* 1.3 62.7 + - - +
111B LEU* 3.7 1.7 - - - +
112B ASP* 3.0 21.8 + - - -
113B SER* 3.0 28.5 + - - +
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Residues in contact with ALA 107 (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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12A GLY* 3.6 2.9 - - - -
13A SER* 2.9 33.2 + - - +
15A PHE* 4.1 13.0 - - + -
39B HIS* 4.0 6.1 - - + -
40B GLY* 3.8 25.1 - - - +
106B SER* 1.3 78.9 + - - +
108B GLY* 1.3 58.7 - - - +
110B TYR 3.4 12.6 - - - +
111B LEU* 4.2 5.8 - - + -
112B ASP* 3.5 6.3 - - - -
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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