Contacts of the strand formed by residues 159 - 166 (chain F) in PDB entry 5ZRV
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 VAL 159 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F VAL 5.1 2.9 + - - -
98F VAL* 5.5 2.2 - - - +
99F ASP* 3.5 15.5 + - - +
100F TYR* 3.3 22.9 + - - -
158F ASP* 1.3 75.6 - - - +
160F ILE* 1.3 59.0 + - - +
320F ILE 3.3 10.5 - - - -
321F MET* 4.7 2.2 - - - +
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Residues in contact with ILE 160 (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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99F ASP 6.1 0.2 - - - -
100F TYR 3.9 9.9 - - - -
148F GLY* 6.1 4.9 - - - -
159F VAL* 1.3 73.4 - - - +
161F VAL* 1.3 61.5 + - - +
162F ALA 4.1 0.6 + - - -
319F LEU* 3.5 3.3 - - - -
320F ILE* 2.8 37.1 + - - +
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Residues in contact with VAL 161 (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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100F TYR 3.9 7.0 + - - +
101F ILE* 4.1 8.3 - - - +
102F ILE* 2.8 29.1 + - - +
160F ILE* 1.3 74.1 - - - +
162F ALA* 1.3 58.8 + - - +
318F MET 3.8 12.1 - - - -
319F LEU* 4.7 0.2 - - - +
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Residues in contact with ALA 162 (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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102F ILE 3.3 5.6 - - - -
144F ALA* 5.3 14.6 - - - +
145F MET* 5.5 2.9 - - - +
160F ILE 4.1 1.0 + - - -
161F VAL* 1.3 74.2 - - - +
163F GLY* 1.3 57.9 + - - +
317F ALA* 3.3 2.2 - - - -
318F MET* 3.0 30.2 + - - +
319F LEU 5.8 0.2 - - - -
435F CYS* 6.1 1.0 - - - -
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Residues in contact with GLY 163 (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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102F ILE 3.3 8.0 + - - -
103F PHE* 3.2 7.1 - - - -
104F GLY* 3.0 23.0 + - - -
141F ALA* 4.7 9.3 - - - -
144F ALA* 5.9 2.8 - - - +
162F ALA* 1.3 75.3 - - - +
164F GLY* 1.3 59.1 + - - -
316F SER 2.9 15.7 - - - -
317F ALA* 3.9 2.5 - - - -
435F CYS* 6.4 1.8 - - - -
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Residues in contact with GLY 164 (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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104F GLY* 3.4 11.2 - - - -
141F ALA* 4.8 5.6 - - - +
163F GLY* 1.3 74.3 - - - -
165F VAL* 1.3 58.5 + - - -
314F GLY 4.1 0.5 - - - +
315F ALA* 3.1 4.5 - - - -
316F SER* 2.9 31.3 + - - +
431F GLY 3.8 15.0 - - - -
432F ALA* 4.2 13.8 + - - -
435F CYS* 6.3 1.4 - - - +
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Residues in contact with VAL 165 (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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76F PRO 5.1 7.0 - - - +
80F ALA* 5.7 9.9 - - - +
104F GLY 3.3 9.1 + - - +
105F THR* 3.9 19.2 - - - -
164F GLY* 1.3 73.7 - - - -
166F GLU* 1.3 59.2 + - - +
314F GLY 3.8 4.5 - - - -
315F ALA* 4.1 4.7 - - - +
431F GLY 4.2 3.7 + - - -
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Residues in contact with GLU 166 (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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76F PRO* 5.6 4.3 - - - -
105F THR* 5.9 0.2 - - - +
164F GLY 4.4 0.2 - - - -
165F VAL* 1.3 75.1 - - - +
167F LEU* 1.3 57.9 + - - +
168F MET 4.2 0.4 - - - -
313F ASP* 3.6 2.1 - - - -
314F GLY 3.0 35.5 + - - +
431F GLY* 5.8 4.1 - - - +
432F ALA* 5.9 0.8 - - - +
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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