Contacts of the strand formed by residues 159 - 166 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97H VAL 5.1 3.9 + - - -
98H VAL* 5.5 2.9 - - - +
99H ASP* 3.5 15.0 + - - +
100H TYR* 3.3 23.0 + - - -
158H ASP* 1.3 77.3 + - - +
160H ILE* 1.3 58.5 + - - +
320H ILE 3.3 10.8 - - - -
321H MET* 4.7 2.2 - - - +
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Residues in contact with ILE 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H TYR 3.9 10.3 - - - -
148H GLY* 6.1 5.4 - - - -
159H VAL* 1.3 75.0 - - - +
161H VAL* 1.3 60.3 + - - +
319H LEU* 3.5 3.6 - - - -
320H ILE* 2.8 37.2 + - - +
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Residues in contact with VAL 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H TYR 3.9 7.2 + - - +
101H ILE* 4.1 8.1 - - - +
102H ILE* 2.8 29.0 + - - +
160H ILE* 1.3 74.4 - - - +
162H ALA* 1.3 58.3 + - - +
318H MET 3.8 12.3 - - - -
319H LEU* 4.7 0.2 - - - +
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Residues in contact with ALA 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ILE 3.3 5.2 - - - -
144H ALA* 5.3 15.0 - - - +
145H MET* 5.5 2.5 - - - +
160H ILE 4.1 1.2 + - - -
161H VAL* 1.3 74.8 - - - +
163H GLY* 1.3 58.3 + - - +
317H ALA* 3.3 2.2 - - - -
318H MET* 3.0 29.3 + - - +
319H LEU* 5.3 0.4 - - - +
435H CYS* 6.1 0.7 - - - -
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Residues in contact with GLY 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H ILE 3.3 8.3 + - - -
103H PHE* 3.2 6.6 - - - -
104H GLY* 3.0 23.7 + - - -
141H ALA* 4.7 10.0 - - - -
144H ALA* 5.9 2.8 - - - +
162H ALA* 1.3 74.8 - - - +
164H GLY* 1.3 58.9 + - - -
316H SER 2.9 14.8 - - - -
317H ALA* 3.9 2.7 - - - -
435H CYS* 6.4 2.0 - - - -
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Residues in contact with GLY 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H GLY* 3.4 10.5 - - - -
141H ALA* 4.8 6.2 - - - +
163H GLY* 1.3 74.8 - - - -
165H VAL* 1.3 58.5 + - - -
166H GLU 4.4 0.2 - - - -
314H GLY 4.1 0.3 - - - +
315H ALA* 3.1 4.5 - - - -
316H SER* 2.9 31.7 + - - +
431H GLY 3.8 14.1 - - - -
432H ALA* 4.2 13.9 + - - -
435H CYS* 6.3 1.6 - - - +
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Residues in contact with VAL 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H PRO 5.1 7.0 - - - +
80H ALA* 5.7 9.6 - - - +
104H GLY 3.3 8.7 + - - +
105H THR* 3.9 19.1 - - - -
164H GLY* 1.3 74.1 - - - -
166H GLU* 1.3 58.4 + - - +
314H GLY 3.8 4.5 - - - -
315H ALA* 4.1 4.9 - - - +
431H GLY 4.2 4.1 + - - -
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H PRO* 5.6 4.5 - - - -
105H THR* 5.9 0.2 - - - +
165H VAL* 1.3 74.0 - - - +
167H LEU* 1.3 58.0 + - - +
168H MET 4.2 0.7 - - - -
313H ASP* 3.6 2.1 - - - -
314H GLY 3.0 36.3 + - - +
431H GLY 5.8 3.8 - - - +
432H 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