Contacts of the strand formed by residues 112 - 117 (chain B) in PDB entry 1VLH
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 GLU 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 2.7 63.8 + - - +
25A SER* 4.4 11.1 + - - +
26A ILE* 3.5 35.9 - - + -
116A LEU* 4.0 13.9 - - + +
82B LYS 2.8 11.7 + - - +
83B VAL* 3.3 6.1 - - + +
84B LEU* 2.9 25.3 + - - +
105B LYS* 3.4 6.5 + - - +
110B ASP 4.8 2.8 - - - +
111B LEU* 1.3 81.7 - - - +
113B THR* 1.3 64.7 + - - +
114B VAL 3.9 0.6 + - - -
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE 3.8 7.1 - - - +
116A LEU* 3.9 11.1 - - - +
117A ILE* 4.5 3.1 + - - +
84B LEU* 3.3 29.4 - - + +
86B ARG* 3.9 19.3 - - + -
101B ALA* 4.0 27.0 + - + +
104B ASN* 5.0 1.2 + - - +
111B LEU* 4.0 10.2 - - - +
112B GLU* 1.3 74.9 + - - +
114B VAL* 1.3 65.7 + - - +
115B PHE* 3.6 31.5 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.6 22.7 - - + -
114A VAL* 3.2 37.9 - - + -
115A PHE 3.4 3.1 - - - -
116A LEU* 3.4 25.4 - - + -
27B PHE* 4.7 15.0 - - + -
83B VAL* 4.4 13.7 - - + -
84B LEU 2.7 12.2 + - - +
85B VAL* 3.3 8.2 - - + +
86B ARG* 2.9 24.9 + - - +
112B GLU 4.6 1.6 - - - +
113B THR* 1.3 73.6 - - - +
115B PHE* 1.3 66.0 + - - +
116B LEU* 5.0 3.8 - - + -
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 4.6 2.0 - - + -
114A VAL* 3.5 7.3 - - - -
115A PHE* 2.9 54.8 + - + +
117A ILE* 3.3 40.6 - - + -
86B ARG* 3.2 32.8 - - + -
88B LEU* 3.6 39.3 - - + -
97B GLU* 3.4 41.5 - - + -
101B ALA* 4.3 0.7 - - + -
113B THR* 3.6 25.4 - - + -
114B VAL* 1.3 74.7 - - - +
116B LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 4.1 10.5 - - - +
113A THR 3.9 7.9 - - - +
114A VAL* 3.9 28.3 - - + -
19B ILE* 3.9 27.1 - - + +
22B ARG* 4.2 17.5 - - + +
23B ALA* 3.8 38.6 - - + +
26B ILE* 4.4 8.1 - - + -
27B PHE* 6.2 1.8 - - + -
85B VAL* 4.2 10.8 - - + -
86B ARG 3.0 7.7 + - - +
87B GLY* 3.3 4.2 - - - -
88B LEU* 2.8 26.2 + - - -
114B VAL* 5.0 3.6 - - + -
115B PHE* 1.3 78.3 - - - +
117B ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.2 39.3 - - + +
101A ALA* 4.0 15.0 - - + -
102A LEU* 4.2 25.0 - - + +
113A THR 4.4 3.7 + - - +
115A PHE* 3.3 33.4 - - + -
19B ILE* 4.5 0.4 - - - -
22B ARG* 2.8 39.7 + - - +
88B LEU* 3.6 30.5 - - + +
116B LEU* 1.3 72.4 - - - +
118B ALA* 1.3 69.6 + - - +
119B SER* 4.6 0.2 - - - -
123B SER* 5.7 0.9 - - - +
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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