Contacts of the strand formed by residues 87 - 95 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F TYR 4.6 3.2 - - - +
86F SER* 1.3 79.9 + - - +
88F LEU* 1.3 73.8 + - - +
89F ALA 4.9 0.7 - - - +
129F ILE* 5.7 0.7 - - + +
130F ARG* 3.4 9.2 + - - +
131F THR* 2.9 54.3 + - - +
133F ASN* 4.2 8.7 - - - +
134F SER* 3.3 37.7 - - - +
137F LEU* 4.0 20.4 - - + -
157F ILE* 3.8 36.6 - - + -
158F VAL 5.7 0.2 - - - +
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E TYR* 3.4 35.0 - - + -
86F SER 4.1 1.6 + - - +
87F MET* 1.3 82.3 - - - +
89F ALA* 1.3 66.9 + - - +
90F PHE* 5.4 0.9 - - + -
128F LYS* 3.6 29.6 - - + -
129F ILE 3.4 17.5 - - - +
130F ARG* 4.0 29.4 - - + +
157F ILE 3.9 0.2 - - - -
158F VAL* 3.0 48.2 + - + +
161F THR* 4.3 5.6 - - - +
164F GLU* 4.1 3.8 - - - +
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Residues in contact with ALA 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F MET* 4.8 1.1 - - + -
88F LEU* 1.3 79.0 - - - +
90F PHE* 1.3 65.8 + - - +
91F ILE 4.0 0.2 - - - -
128F LYS* 3.6 5.7 - - - +
129F ILE* 3.0 47.3 + - + +
137F LEU* 4.3 13.0 - - + -
155F THR* 3.7 26.9 - - + -
156F MET 3.5 7.6 - - - +
157F ILE* 4.2 4.7 - - + -
158F VAL* 4.4 1.1 - - - +
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Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E PHE* 3.7 25.8 - + - -
115E GLU* 4.4 1.1 - - - -
117E TYR* 3.6 34.3 - + - -
119E THR* 4.7 0.9 - - + -
126E VAL* 4.3 22.2 - - + -
88F LEU* 5.3 0.7 - - + -
89F ALA* 1.3 72.8 - - - +
91F ILE* 1.3 61.7 + - - +
92F LEU 3.8 0.4 + - - -
115F GLU* 4.9 0.4 - - - -
126F VAL* 3.6 23.8 - - + -
127F VAL 3.2 8.1 - - - +
128F LYS* 3.5 38.4 - - + -
154F HIS 3.7 1.0 - - - +
155F THR* 3.6 0.5 - - - -
156F MET* 2.7 63.9 + - + +
158F VAL* 3.9 19.3 - - + -
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Residues in contact with ILE 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F PHE* 1.3 73.4 - - - +
92F LEU* 1.3 65.5 + - - +
93F VAL* 3.8 8.7 + - + +
125F MET 3.6 2.1 - - - +
126F VAL* 3.7 0.3 - - - -
127F VAL* 2.8 45.1 + - + +
129F ILE* 3.6 35.9 - - + -
137F LEU* 4.5 3.8 - - + -
141F LEU* 3.9 14.4 - - + +
144F ILE* 3.6 28.3 - - + -
153F THR* 3.7 35.7 - - + -
154F HIS 3.7 2.7 - - - +
155F THR* 3.9 18.4 - - + +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E LEU* 5.8 4.3 - - + -
156E MET* 4.4 15.3 - - + -
90F PHE* 5.4 0.2 - - + -
91F ILE* 1.3 74.1 - - - +
93F VAL* 1.3 60.2 + - - +
123F TYR* 3.6 40.3 - - + -
125F MET 3.3 3.6 - - - +
126F VAL* 3.7 30.5 - - + -
153F THR* 3.1 7.1 - - - -
154F HIS* 2.8 54.8 + - + +
156F MET* 4.0 35.9 - - + -
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 3.8 23.6 - - + +
92F LEU* 1.3 77.9 - - - +
94F LYS* 1.3 72.6 + - - +
95F VAL* 3.8 8.2 + - + +
103F VAL* 4.6 5.4 - - + -
107F LEU* 4.7 4.9 - - + -
123F TYR* 4.0 2.8 - - - +
124F ASP* 2.9 25.6 + - - +
125F MET* 2.9 24.3 + - + +
127F VAL* 4.1 18.6 - - + -
144F ILE* 4.7 6.1 - - + -
150F VAL* 3.9 30.1 - - + -
152F GLY 3.5 2.9 - - - +
153F THR* 4.4 4.5 - - + -
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Residues in contact with LYS 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL* 1.3 73.0 - - - +
95F VAL* 1.3 58.1 + - - +
122F ASP* 3.6 46.7 + - - +
123F TYR* 3.6 34.6 + - + -
124F ASP* 3.7 5.8 - - - +
150F VAL* 3.4 5.4 - - - -
151F GLU* 2.7 49.8 + - + +
152F GLY* 2.8 26.2 + - - +
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL* 4.1 7.2 - - + +
94F LYS* 1.3 76.7 - - - +
96F LYS* 1.3 72.0 + - - +
97F ALA* 3.1 4.9 + - - -
99F LYS* 3.7 5.6 - - + -
100F TYR* 3.5 44.5 + - + +
103F VAL* 3.7 17.0 - - + -
124F ASP* 2.9 25.8 + - + +
125F MET* 3.6 31.4 - - + -
149F GLY 3.2 9.4 - - - +
151F GLU* 4.1 9.0 - - - +
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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