Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 1NBN
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A SER* 3.2 9.3 + - - -
93A LYS* 4.8 0.9 - - - +
94A SER* 3.0 50.9 + - - +
95A PRO 3.2 17.8 + - - -
96A VAL* 4.0 8.6 - - + +
97A THR 5.0 0.4 - - - +
100A GLN* 3.5 16.2 + - - +
101A PRO* 1.3 73.4 + - - +
103A ILE* 1.3 76.6 + - - +
151A THR* 3.9 0.5 - - - -
152A LEU* 2.9 36.1 + - + -
154A PRO* 3.9 14.5 - - + +
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Residues in contact with ILE 103 (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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92A SER* 3.5 5.2 + - - -
93A LYS* 3.0 61.6 + - + +
102A ASN* 1.3 87.0 + - - +
104A LEU* 1.3 61.4 + - - +
149A TYR* 4.0 27.1 - - + -
150A LEU 3.4 15.3 - - - +
151A THR* 4.2 20.6 - - + +
152A LEU* 4.7 0.4 - - - -
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Residues in contact with LEU 104 (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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90A VAL* 4.1 4.3 - - + -
91A PHE 3.9 5.6 - - - -
92A SER* 3.9 27.6 - - - +
96A VAL* 4.8 3.4 - - + -
103A ILE* 1.3 72.6 - - - +
105A ILE* 1.3 61.1 + - - +
120A TRP* 3.7 22.3 - - + -
149A TYR* 3.5 5.5 - - - -
150A LEU* 3.1 32.1 + - + -
152A LEU* 3.7 22.6 - - + +
160A TYR* 3.7 37.7 - - + -
177A TRP* 3.7 42.2 - - + -
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Residues in contact with ILE 105 (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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89A THR 3.8 0.3 - - - +
90A VAL* 3.4 7.8 - - - +
91A PHE* 2.9 77.7 + - + +
93A LYS* 3.6 30.5 - - + +
104A LEU* 1.3 73.2 - - - +
106A CYS* 1.3 64.2 + - - +
107A LEU* 3.8 4.7 + - + +
120A TRP* 4.0 2.2 - - - -
147A ILE* 3.7 27.8 - - + -
148A SER 3.8 2.7 - - - -
149A TYR* 3.9 13.5 - - + +
148B ASN* 3.3 25.1 - - + +
154B GLN* 3.8 5.2 - - - +
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Residues in contact with CYS 106 (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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88A VAL* 4.2 4.5 - - - -
89A THR 3.5 5.4 - - - -
90A VAL* 3.7 9.4 - - + -
105A ILE* 1.3 72.8 - - - +
107A LEU* 1.3 60.4 + - - +
108A VAL* 3.3 25.9 + - + -
118A ILE* 4.3 5.2 - - + -
120A TRP* 3.7 15.2 - - + -
146A LYS 3.7 1.9 - - - +
147A ILE* 3.5 5.5 - - - -
148A SER* 2.9 34.7 + - - +
162A CYS* 2.0 49.4 - - - -
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Residues in contact with LEU 107 (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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87A GLU* 3.2 21.1 - - - +
89A THR* 2.9 39.0 + - + +
91A PHE* 4.0 31.0 - - + -
105A ILE* 3.8 6.8 + - + +
106A CYS* 1.3 67.8 - - - +
108A VAL* 1.3 58.5 + - - +
109A ASP* 4.8 4.3 - - + +
145A PHE* 4.0 24.5 - - + -
147A ILE* 4.1 19.7 - - + -
146B ILE* 5.6 2.0 - - + -
147B ARG 4.5 13.9 - - - +
148B ASN* 6.2 0.2 - - - -
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Residues in contact with VAL 108 (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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86A PRO* 4.1 8.3 - - + -
87A GLU 3.5 3.4 - - - +
88A VAL* 4.5 4.7 - - + -
106A CYS* 3.3 37.7 + - - +
107A LEU* 1.3 69.4 - - - +
109A ASP* 1.3 63.3 + - - +
111A ILE* 3.8 26.2 - - + +
118A ILE* 4.0 16.6 - - + -
144A PHE 4.2 0.3 - - - +
145A PHE* 3.3 10.0 - - - -
146A LYS 3.2 33.8 + - - +
147A ILE* 4.3 2.2 - - - +
162A CYS* 4.0 1.1 - - - -
164A VAL* 3.8 29.6 - - + -
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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