Contacts of the strand formed by residues 133 - 137 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 3.0 13.7 + - - +
97B VAL* 3.3 11.7 - - + +
98B ILE 3.1 21.0 + - - -
131B GLN 4.5 5.6 - - - +
132B ALA* 1.3 73.2 - - - +
134B ILE* 1.3 60.8 + - - +
169B ASN* 4.0 23.1 - - + +
171B GLN* 5.8 0.6 + - - +
216B LEU* 3.5 56.0 - - + +
219B GLU* 4.4 14.6 - - + +
220B THR* 6.0 2.2 - - - +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.3 13.7 - - + +
100B VAL* 4.4 12.6 - - + -
122B VAL* 3.8 25.4 - - + +
125B ILE* 3.5 32.8 - - + -
126B ASN* 4.1 17.5 - - + +
132B ALA 4.2 7.0 - - - +
133B LYS* 1.3 75.9 - - - +
135B ILE* 1.3 72.9 + - - +
136B VAL* 4.3 8.3 - - + -
169B ASN 2.9 22.2 + - - +
170B VAL* 3.4 16.4 - - + -
171B GLN* 3.1 26.3 + - - +
216B LEU* 5.7 0.8 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.9 17.3 - - + -
98B ILE 2.9 7.7 + - - +
99B VAL* 3.3 12.7 - - + +
100B VAL* 2.8 26.5 + - - +
134B ILE* 1.3 77.7 - - - +
136B VAL* 1.3 69.6 + - - +
137B LEU* 4.0 3.9 + - + +
171B GLN* 3.5 7.4 - - + +
173B LEU* 4.0 26.7 - - + -
209B LEU* 4.2 13.0 - - + -
212B LEU* 3.7 28.5 - - + -
213B ILE* 3.7 30.5 - - + -
216B LEU* 4.0 14.8 - - + -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 3.4 26.7 - - + +
101B TRP* 5.9 0.2 - - - -
118B ILE* 4.2 22.2 - - + -
122B VAL* 4.0 24.7 - - + -
134B ILE* 4.1 5.8 - - + -
135B ILE* 1.3 73.9 - - - +
137B LEU* 1.3 74.7 + - - +
138B GLY 3.6 0.5 + - - -
160B LEU* 4.4 5.4 - - + -
164B LEU* 4.2 14.6 - - + -
170B VAL* 4.6 1.1 - - + -
171B GLN 2.9 12.2 + - - +
172B LEU* 3.3 15.6 - - + +
173B LEU 2.8 27.4 + - - -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 5.6 0.4 - - + -
53B MET* 5.1 1.6 - - + -
99B VAL* 3.7 28.0 - - + -
100B VAL 2.9 8.0 + - - +
101B TRP* 3.3 56.7 - - + +
102B VAL 5.1 1.4 + - - +
118B ILE* 5.8 0.9 - - - +
135B ILE* 3.9 1.5 - - + -
136B VAL* 1.3 82.4 - - - +
138B GLY* 1.3 64.0 + - - +
139B LEU* 3.9 2.9 + - - +
160B LEU* 5.9 0.2 - - - +
173B LEU* 3.4 26.2 - - + +
175B THR* 4.1 10.5 - - - +
205B ILE* 4.9 7.9 - - + -
209B LEU* 3.7 37.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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