Contacts of the strand formed by residues 133 - 137 (chain R) in PDB entry 1VYH
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 LYS 133 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96R LYS 3.0 12.2 + - - +
97R VAL* 3.2 9.5 - - + +
98R ILE 3.0 21.7 + - - +
131R GLN 4.3 7.2 - - - +
132R ALA* 1.3 74.0 - - - +
134R ILE* 1.3 60.7 + - - +
169R ASN* 4.0 20.0 - - + +
216R LEU* 3.3 56.0 - - + +
219R GLU* 3.7 22.1 - - + +
220R THR* 5.7 2.2 + - - +
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Residues in contact with ILE 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ILE* 3.3 15.7 - - + +
100R VAL* 4.3 18.6 - - + -
122R VAL* 4.6 11.0 - - + +
125R ILE* 4.0 23.3 - - + -
126R ASN* 4.0 27.1 - - + +
132R ALA 3.9 10.5 - - - +
133R LYS* 1.3 76.8 - - - +
135R ILE* 1.3 73.1 + - - +
136R VAL* 4.5 2.9 - - + -
168R ALA 4.1 2.2 - - - +
169R ASN 3.0 24.4 + - - +
170R VAL* 3.4 22.0 - - + -
171R GLN* 3.0 30.0 + - - +
216R LEU* 5.5 1.6 - - - +
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Residues in contact with ILE 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97R VAL* 4.2 7.0 - - + -
98R ILE 2.8 11.0 + - - +
99R VAL* 3.3 6.0 - - + -
100R VAL* 2.7 32.4 + - - -
133R LYS 4.1 0.6 + - - -
134R ILE* 1.3 77.1 - - - +
136R VAL* 1.3 60.8 + - - +
137R LEU* 3.7 28.7 - - + -
171R GLN* 3.5 8.1 - - + +
173R LEU* 4.3 10.1 - - + -
209R LEU* 4.0 12.1 - - + -
212R LEU* 3.8 31.9 - - + -
213R ILE* 3.6 31.4 - - + -
216R LEU* 4.0 17.5 - - + -
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Residues in contact with VAL 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R VAL* 3.4 22.7 - - + +
101R TRP* 5.7 0.4 - - - -
102R VAL 6.2 0.4 - - - +
118R ILE* 4.1 22.4 - - + -
122R VAL* 3.8 28.7 - - + -
134R ILE* 4.5 4.0 - - + -
135R ILE* 1.3 77.7 - - - +
137R LEU* 1.3 71.9 + - - +
138R GLY 3.6 0.7 + - - -
160R LEU* 4.4 14.6 - - + -
164R LEU* 4.2 14.1 - - + -
170R VAL* 4.6 3.6 - - + -
171R GLN 2.9 13.9 + - - +
172R LEU* 3.3 5.6 - - + +
173R LEU 2.8 30.5 + - - -
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Residues in contact with LEU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99R VAL* 4.8 6.3 - - + -
100R VAL 2.9 8.0 + - - +
101R TRP* 3.0 70.9 - - + -
102R VAL 5.1 0.9 + - - +
135R ILE* 3.7 22.4 - - + -
136R VAL* 1.3 81.5 - - - +
138R GLY* 1.3 61.6 + - - +
139R LEU* 4.9 2.8 - - - +
140R LEU* 6.1 0.4 - - + -
173R LEU* 3.4 19.7 - - + +
175R THR* 4.6 9.6 - - - +
205R ILE* 3.8 20.6 - - + +
209R LEU* 3.8 20.6 - - + -
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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