Contacts of the strand formed by residues 87 - 95 (chain G) in PDB entry 2ZNZ
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 MET 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85G TYR 3.3 3.5 - - - +
86G SER* 1.3 80.0 - - - +
88G LEU* 1.3 78.8 + - - +
89G ALA* 5.2 0.7 - - + +
129G ILE* 5.8 0.7 - - + +
130G ARG* 3.4 8.1 + - - +
131G THR* 2.9 57.5 + - + +
133G ASN* 4.0 11.4 - - - +
134G SER* 3.6 36.1 - - - +
137G LEU* 3.9 22.4 - - + -
157G ILE* 4.1 24.2 - - + -
158G VAL 5.8 0.2 - - - +
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G SER 4.2 1.0 + - - -
87G MET* 1.3 82.2 - - - +
89G ALA* 1.3 66.6 + - - +
90G PHE* 5.4 0.9 - - + -
128G LYS* 3.6 27.8 - - + -
129G ILE 3.4 16.8 - - - +
130G ARG* 3.7 28.5 - - + +
157G ILE* 3.9 1.6 - - - -
158G VAL* 3.0 49.0 + - + +
161G THR* 4.1 4.9 - - - +
164G GLU* 3.9 9.9 - - - +
117H TYR* 3.4 36.1 - - + -
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Residues in contact with ALA 89 (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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87G MET* 4.8 0.7 - - + -
88G LEU* 1.3 80.0 - - - +
90G PHE* 1.3 65.2 + - - +
91G ILE 4.0 0.4 - - - -
128G LYS* 3.5 6.1 - - - +
129G ILE* 3.0 50.2 + - + +
137G LEU* 4.2 10.3 - - + -
155G THR* 3.9 21.1 - - + -
156G MET 3.4 11.4 - - - +
157G ILE* 4.3 7.6 - - + -
158G VAL* 4.4 2.0 - - - +
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Residues in contact with PHE 90 (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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88G LEU* 5.3 0.7 - - + -
89G ALA* 1.3 72.5 - - - +
91G ILE* 1.3 62.2 + - - +
92G LEU* 3.9 4.9 + - + +
126G VAL* 3.8 23.3 - - + -
127G VAL 3.2 8.5 - - - -
128G LYS* 3.6 32.1 - - + -
154G HIS 3.9 0.3 - - - +
155G THR* 3.5 1.4 - - - +
156G MET* 2.7 54.7 + - + +
158G VAL* 4.0 20.0 - - + -
90H PHE* 3.8 24.5 - + - -
115H GLU* 4.5 0.2 - - - -
117H TYR* 3.5 42.8 - + - -
119H THR* 4.6 2.0 - - + -
126H VAL* 4.1 26.0 - - + -
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Residues in contact with ILE 91 (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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90G PHE* 1.3 73.0 - - - +
92G LEU* 1.3 64.7 + - - +
93G VAL* 3.8 8.8 + - + +
125G MET 3.6 0.9 - - - +
126G VAL* 3.6 2.9 - - - -
127G VAL* 2.7 51.6 + - + +
129G ILE* 3.8 35.0 - - + -
137G LEU* 4.7 1.6 - - + -
141G LEU* 3.7 19.5 - - + -
144G ILE* 3.8 21.3 - - + -
153G THR* 3.6 37.5 - - + -
154G HIS 3.8 2.2 - - - -
155G THR* 3.7 19.1 - - + +
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Residues in contact with LEU 92 (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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90G PHE* 4.9 5.8 - - + +
91G ILE* 1.3 74.4 - - - +
93G VAL* 1.3 58.8 + - - +
123G TYR* 3.6 41.3 - - + -
125G MET 3.4 4.0 - - - +
126G VAL* 3.9 26.2 - - + -
153G THR* 3.2 6.9 - - - -
154G HIS* 2.7 52.9 + - + +
156G MET* 3.8 37.9 - - + -
92H LEU* 5.7 2.9 - - + -
156H MET* 4.5 16.4 - - + -
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Residues in contact with VAL 93 (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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91G ILE* 3.8 24.5 - - + +
92G LEU* 1.3 77.8 - - - +
94G LYS* 1.3 67.3 + - - +
95G VAL* 3.8 12.2 + - + +
103G VAL* 4.9 4.7 - - + -
107G LEU* 4.9 4.5 - - + -
123G TYR* 3.9 3.8 - - - +
124G ASP* 2.7 31.4 + - - +
125G MET* 2.9 26.3 + - + +
127G VAL* 3.9 21.3 - - + -
144G ILE* 5.1 4.9 - - + -
150G VAL* 4.0 23.3 - - + -
152G GLY 3.6 7.2 - - - +
153G THR* 4.5 2.9 - - + -
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Residues in contact with LYS 94 (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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93G VAL* 1.3 71.9 - - - +
95G VAL* 1.3 61.5 + - - +
122G ASP 3.2 22.2 + - - +
123G TYR* 3.8 20.2 - - + -
124G ASP* 3.1 25.2 + - - +
150G VAL* 3.6 5.5 - - - -
151G GLU* 2.8 50.6 + - + +
152G GLY* 2.9 28.3 + - - +
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Residues in contact with VAL 95 (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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93G VAL* 4.1 11.4 - - + +
94G LYS* 1.3 80.2 + - - +
96G LYS* 1.3 77.1 + - - +
97G ALA* 3.6 1.7 + - - -
99G LYS* 4.0 5.2 - - + +
100G TYR* 3.8 48.3 + - + +
103G VAL* 4.4 8.3 - - + -
124G ASP* 2.9 21.5 + - + +
125G MET* 3.8 35.7 - - + -
149G GLY 3.3 7.2 - - - +
151G GLU* 4.1 8.0 - - - +
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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