Contacts of the strand formed by residues 80 - 87 (chain G) in PDB entry 1NJI
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 TRP 80 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G ASN* 3.1 59.4 + - - -
74G HIS* 3.7 31.4 - + + -
75G GLY* 3.5 8.1 - - - -
79G GLY* 1.3 70.2 - - - -
81G GLU* 1.3 62.9 + - - +
82G TYR* 4.9 3.4 - - + -
133G VAL 4.3 0.2 - - - -
134G SER* 2.8 27.2 - - - -
135G GLY 2.9 25.4 + - - +
136G PRO 3.7 8.3 + - - -
138G ILE* 3.5 47.2 - - + +
141G VAL* 4.0 13.6 - - + +
172G PRO* 3.6 38.6 - - + -
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Residues in contact with GLU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G GLU 5.9 1.3 - - - +
79G GLY 4.3 2.8 + - - -
80G TRP* 1.3 74.7 - - - +
82G TYR* 1.3 64.6 + - - +
132G THR* 4.1 16.7 + - - +
133G VAL 3.0 6.5 - - - +
134G SER* 3.3 26.5 + - - -
170G ARG* 4.1 12.4 + - - +
171G LYS 4.6 0.2 - - - -
172G PRO* 3.4 27.9 - - - +
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Residues in contact with TYR 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2780A C 5.1 0.2 - - - -
2781A U 2.7 35.8 + - - -
80G TRP* 4.9 2.2 - - + -
81G GLU* 1.3 78.8 - - - +
83G GLY* 1.3 61.4 + - - +
84G MET* 4.1 0.4 + - - -
131G LEU 3.9 0.2 - - - +
132G THR* 3.4 4.3 + - - -
133G VAL* 2.7 38.4 + - + +
138G ILE* 4.1 11.8 - - + +
141G VAL* 3.5 22.4 - - + -
142G GLY* 3.7 28.2 - - - -
145G ALA* 3.9 26.9 - - + -
168G ILE* 4.1 22.2 - - + -
170G ARG* 3.4 6.1 - - - +
171G LYS* 4.4 8.7 - - + -
172G PRO* 3.6 32.4 - - + +
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Residues in contact with GLY 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G TYR* 1.3 75.0 - - - +
84G MET* 1.3 56.4 + - - +
131G LEU 3.5 6.3 - - - -
168G ILE* 3.4 3.3 - - - +
169G THR* 2.4 37.4 + - - -
170G ARG* 3.0 39.7 + - - +
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Residues in contact with MET 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G TYR 4.8 0.4 - - - +
83G GLY* 1.3 80.4 - - - +
85G GLU* 1.3 65.1 + - - +
130G GLU* 3.4 6.4 - - - +
131G LEU* 2.7 57.1 + - + +
133G VAL* 3.1 33.9 - - + -
145G ALA* 3.7 7.2 - - - +
148G ILE* 3.1 45.5 - - + -
149G GLU 4.9 1.3 - - - -
166G VAL* 3.8 9.0 - - + -
167G TYR 3.0 14.6 - - - +
168G ILE* 3.6 28.0 - - + -
169G THR* 3.7 1.3 - - - -
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Residues in contact with GLU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G MET* 1.3 77.4 - - - +
86G VAL* 1.3 66.8 + - - +
87G PHE* 3.7 3.6 + - + +
129G GLU* 3.5 16.6 - - - +
130G GLU* 4.4 13.5 - - + +
165G GLY 3.7 1.4 - - - +
166G VAL* 3.4 5.2 - - - -
167G TYR* 2.9 34.1 + - + +
169G THR* 3.3 28.1 + - + +
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Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G MET 4.3 0.4 + - - -
85G GLU* 1.3 80.3 - - - +
87G PHE* 1.3 66.8 + - - +
88G TYR* 4.6 1.6 - - + -
93G MET* 3.6 38.8 - - + +
95G VAL* 4.1 20.9 - - + -
126G ILE* 5.8 2.5 - - + -
128G GLY 4.1 4.0 - - - +
129G GLU* 3.2 57.5 + - - +
130G GLU 5.8 0.9 - - - -
131G LEU* 5.5 5.0 - - + +
165G GLY 4.0 3.1 - - - -
166G VAL* 4.1 10.6 - - + +
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Residues in contact with PHE 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G GLU* 4.5 4.5 - - + +
86G VAL* 1.3 79.7 - - - +
88G TYR* 1.3 86.3 + - - +
89G SER* 4.9 9.2 - - - -
93G MET* 3.2 5.7 - - - +
163G GLN* 3.9 40.6 - - + -
164G ASP* 3.2 2.5 - - - -
165G GLY 2.9 38.2 + - - +
167G TYR* 4.9 7.0 - + + -
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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