Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 2NBR
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 ARG 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS* 1.3 75.0 - - - +
89A LEU* 1.3 59.3 + - - +
90A ARG* 3.3 9.9 - - - +
103A GLU* 2.9 41.7 + - + +
104A LEU 3.6 8.1 - - - +
105A SER* 5.1 5.2 - - - -
125A VAL* 3.5 3.5 - - - +
126A LEU* 2.8 64.1 + - + +
127A GLU* 3.1 34.4 + - + +
130A TRP* 3.5 2.6 - - - +
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Residues in contact with LEU 89 (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 ARG* 1.3 74.2 - - - +
90A ARG* 1.3 69.8 + - - +
91A LEU* 4.0 19.5 - - + -
102A MET 4.6 0.2 - - - -
103A GLU* 3.2 6.1 - - - +
104A LEU* 2.9 36.5 + - + +
123A LEU* 3.8 26.2 - - + -
124A HIS 3.4 11.2 - - - +
125A VAL* 3.6 27.8 - - + -
126A LEU* 4.3 0.8 - - - +
130A TRP* 3.6 24.0 - - + +
145A LEU* 4.1 8.1 - - + -
166A LEU* 3.9 35.2 - - + -
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Residues in contact with ARG 90 (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 ARG* 3.3 16.2 - - - +
89A LEU* 1.3 79.3 - - - +
91A LEU* 1.3 61.7 + - - +
92A TYR* 3.4 35.8 + - + +
101A MET* 3.8 17.4 - - + +
102A MET 3.5 3.8 - - - -
103A GLU* 3.0 40.6 + - + +
123A LEU* 3.2 10.7 - - - +
124A HIS* 2.9 42.3 + - + +
126A LEU* 3.6 34.4 - - + +
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Residues in contact with LEU 91 (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 LEU* 4.0 21.3 - - + -
90A ARG* 1.3 74.8 - - - +
92A TYR* 1.3 59.7 + - - +
100A LEU 3.3 2.1 - - - +
101A MET* 3.2 6.6 - - - -
102A MET* 2.9 53.0 + - + +
103A GLU 5.0 0.2 - - - -
104A LEU* 4.0 24.9 - - + -
111A ILE* 3.9 30.3 - - + -
115A PHE* 5.5 7.0 - - + -
117A LEU* 5.4 4.7 - - + +
120A ILE* 3.7 31.2 - - + -
123A LEU* 3.7 16.6 - - + -
166A LEU* 5.5 1.8 - - + -
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Residues in contact with TYR 92 (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 ARG* 3.4 49.6 + - + -
91A LEU* 1.3 72.6 - - - +
93A GLU* 1.3 64.1 + - - +
94A ARG 3.5 6.5 + - - +
97A HIS* 3.5 55.0 - + + +
98A LYS 3.6 6.5 - - - +
99A GLY 5.3 0.4 - - - -
100A LEU 3.4 3.1 - - - -
101A MET* 3.5 28.6 - - + +
117A LEU* 5.6 1.1 - - - -
120A ILE* 3.6 6.4 - - - +
121A ARG 3.5 20.1 + - - -
122A SER* 3.0 34.9 + - - +
124A HIS* 3.6 15.2 + - + +
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Residues in contact with GLU 93 (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 TYR* 1.3 72.6 - - - +
94A ARG* 1.3 67.5 + - + +
98A LYS 3.5 1.2 + - - -
99A GLY* 4.1 2.0 - - - -
100A LEU* 2.9 55.3 + - + +
117A LEU* 3.7 34.7 - - + +
119A GLU 5.1 4.9 - - - +
120A ILE* 6.2 0.4 - - - +
121A ARG* 3.1 19.5 + - - +
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Residues in contact with ARG 94 (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 TYR* 3.5 2.6 - - - +
93A GLU* 1.3 84.8 - - + +
95A GLU* 1.3 59.5 + - - +
98A LYS* 3.0 64.7 + - + +
99A GLY* 4.0 19.0 - - - +
121A ARG* 3.6 7.2 - - - -
122A SER* 2.8 21.1 + - - -
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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