Contacts of the strand formed by residues 111 - 120 (chain A) in PDB entry 2NUO
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 2.9 51.5 + - + +
30A ASP 3.5 2.2 + - - -
31A ALA* 4.6 6.7 - - - +
32A ILE* 3.8 24.5 - - + -
39A HIS 4.6 1.3 - - - +
68A TYR* 3.6 4.9 - - - +
69A ILE* 2.9 41.2 + - + -
106A SER 3.7 3.1 - - - +
107A ALA* 4.4 4.5 - - + -
110A TYR* 1.3 70.6 - - - +
112A ASP* 1.3 57.4 + - - +
113A SER 3.6 18.8 - - - +
114A LEU* 4.0 16.6 - - + -
15B PHE* 3.7 26.7 - - + -
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Residues in contact with ASP 112 (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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67A ASP 3.5 6.6 - - - +
68A TYR* 3.6 21.7 - - - +
69A ILE* 4.1 1.1 - - - -
106A SER 3.0 8.9 + - - +
107A ALA* 3.6 0.3 - - - -
108A GLY 3.3 13.0 + - - -
111A LEU* 1.3 72.2 - - - +
113A SER* 1.3 61.1 + - - +
301A BGC 2.6 49.1 + - - -
8B GLY* 3.4 4.5 - - - -
9B GLY 3.0 23.1 + - - +
11B GLY* 3.2 37.4 + - - +
12B GLY* 3.4 4.7 - - - -
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Residues in contact with SER 113 (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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69A ILE* 4.0 4.0 - - - -
105A GLY* 3.2 3.8 - - - -
106A SER* 3.0 46.0 + - - +
111A LEU* 3.4 10.7 - - - +
112A ASP* 1.3 79.8 - - - +
114A LEU* 1.3 60.4 + - - +
6B LYS* 2.9 41.4 + - - +
7B PHE 3.0 11.2 - - - -
9B GLY 3.7 4.0 + - - -
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Residues in contact with LEU 114 (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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29A LEU* 5.1 0.2 - - + -
32A ILE* 4.2 11.7 - - + -
63A ILE* 4.2 17.7 - - + -
69A ILE* 4.0 18.1 - - + +
72A ILE* 4.0 26.7 - - + -
103A ILE* 3.7 26.9 - - + -
104A ASN 3.6 5.4 - - - +
105A GLY* 4.3 0.2 - - - -
111A LEU* 4.0 31.2 - - + -
113A SER* 1.3 79.7 - - - +
115A ASP* 1.3 59.1 + - - +
116A ILE* 3.9 14.8 - - + -
5B ARG 3.6 1.7 - - - +
6B LYS* 3.3 5.3 - - - +
7B PHE* 2.8 34.4 + - + +
15B PHE* 4.6 0.9 - - + -
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Residues in contact with ASP 115 (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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103A ILE* 3.9 0.3 - - - -
104A ASN* 2.9 50.1 + - + +
105A GLY* 3.9 4.0 - - - +
114A LEU* 1.3 72.4 - - - +
116A ILE* 1.3 59.3 + - - +
117A TYR* 3.6 18.0 + - - -
4B HIS* 3.1 33.5 + - - -
5B ARG 3.5 13.5 - - - +
6B LYS* 4.0 14.1 + - + +
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Residues in contact with ILE 116 (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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61A MET* 4.0 21.1 - - + -
63A ILE* 4.2 8.5 - - + -
72A ILE* 6.0 0.2 - - + -
95A LEU* 4.2 4.3 - - + -
100A VAL* 4.0 30.5 - - + -
102A GLN 3.8 1.8 - - - -
103A ILE* 4.1 24.2 - - + -
114A LEU* 4.1 17.9 - - + -
115A ASP* 1.3 74.2 - - - +
117A TYR* 1.3 60.9 + - - +
118A TYR* 3.3 18.9 - - + -
4B HIS* 3.0 5.4 - - - +
5B ARG 2.9 33.4 + - - +
7B PHE* 3.8 29.2 - - + -
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Residues in contact with TYR 117 (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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2A LEU* 3.9 30.5 - - + -
100A VAL* 3.7 2.1 - - - +
101A ILE* 2.8 28.9 + - + -
102A GLN* 3.0 26.6 + - + +
104A ASN* 3.7 24.0 + - - -
115A ASP* 3.6 33.6 + - - -
116A ILE* 1.3 69.9 - - - +
118A TYR* 1.3 62.1 + - - +
3B THR 3.4 3.1 - - - +
4B HIS* 3.4 30.7 - + + -
99B LYS* 4.7 6.2 + - - -
101B ILE* 3.6 30.4 - - + +
119B GLU* 2.7 29.3 + - + -
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Residues in contact with TYR 118 (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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2A LEU* 4.3 2.5 - - - +
95A LEU* 3.6 26.5 - - + +
98A VAL* 3.6 22.0 - - + -
99A LYS 3.3 14.4 - - - +
100A VAL* 3.9 13.5 - - + +
101A ILE* 4.0 9.2 - - - -
116A ILE* 3.3 30.3 - - + -
117A TYR* 1.3 73.7 - - - +
119A GLU* 1.3 65.4 + - - +
120A GLN* 3.6 25.4 + - + -
1B SER 3.6 0.5 - - - +
2B LEU* 3.6 1.6 - - - -
3B THR* 2.9 58.0 + - + +
4B HIS 4.9 0.2 + - - -
5B ARG* 3.8 32.1 - - + +
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Residues in contact with GLU 119 (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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98A VAL* 3.2 8.5 - - - +
99A LYS* 2.9 41.3 + - + +
101A ILE* 3.9 4.4 - - + +
118A TYR* 1.3 74.7 - - - +
120A GLN* 1.3 60.0 + - - +
121A TYR* 3.1 43.1 + - + +
0B ACE 3.9 18.6 - - - +
1B SER 3.4 12.3 - - - +
2B LEU* 4.0 22.2 + - + +
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Residues in contact with GLN 120 (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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95A LEU* 4.6 5.4 - - - +
96A SER 2.9 25.1 + - - +
97A ASN* 3.2 8.1 + - - +
98A VAL* 3.4 14.7 - - - +
118A TYR* 3.6 21.2 + - + -
119A GLU* 1.3 72.0 - - - +
121A TYR* 1.3 84.3 + - - +
0B ACE 3.2 4.4 - - - +
1B SER* 2.8 40.4 + - - +
3B THR* 4.6 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