Contacts of the strand formed by residues 112 - 117 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C LYS 2.9 12.4 + - - +
83C VAL* 3.3 8.2 - - + +
84C LEU 2.9 24.9 + - - +
105C LYS* 2.8 23.9 + - - +
110C ASP 4.9 2.2 - - - +
111C LEU* 1.3 74.9 - - - +
113C THR* 1.3 66.5 + - - +
114C VAL* 3.9 1.6 - - + -
22F ARG* 2.7 56.1 + - - +
25F SER* 5.7 3.8 - - - -
26F ILE* 4.0 23.6 - - + -
116F LEU* 3.9 22.1 - - + +
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.4 31.0 - - + +
86C ARG* 4.1 17.5 - - + -
101C ALA* 4.1 27.5 + - + +
104C ASN* 5.1 0.3 + - - -
111C LEU* 4.1 9.4 - - - +
112C GLU* 1.3 76.2 + - - +
114C VAL* 1.3 61.9 + - - +
115C PHE* 3.6 31.4 - - + -
115F PHE 3.7 8.3 - - - +
116F LEU* 3.8 14.9 - - - +
117F ILE* 4.3 4.1 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 4.4 17.3 - - + -
83C VAL* 4.1 16.2 - - + -
84C LEU 2.8 9.5 + - - +
85C VAL* 3.2 8.4 - - + +
86C ARG 2.9 24.1 + - - -
112C GLU* 4.7 2.0 - - + +
113C THR* 1.3 75.0 - - - +
115C PHE* 1.3 68.6 + - - +
116C LEU* 4.8 4.0 - - + -
26F ILE* 3.6 22.2 - - + -
114F VAL* 3.5 31.9 - - + -
115F PHE 3.4 2.7 - - - -
116F LEU* 3.6 24.0 - - + -
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Residues in contact with PHE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ARG* 3.1 32.3 - - + +
88C LEU* 3.6 47.8 - - + -
97C GLU* 3.5 35.9 - - + -
98C LEU* 5.6 0.4 - - + -
101C ALA* 4.5 0.2 - - + -
113C THR* 3.6 24.0 - - + -
114C VAL* 1.3 74.4 - - - +
116C LEU* 1.3 62.9 + - - +
88F LEU* 4.7 0.2 - - + -
114F VAL* 3.5 7.4 - - - -
115F PHE* 2.9 49.3 + - + +
117F ILE* 3.4 37.7 - - + -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.9 26.9 - - + +
22C ARG* 3.9 18.2 - - + +
23C ALA* 3.8 35.9 - - + +
26C ILE* 4.0 10.5 - - + -
27C PHE* 6.3 0.7 - - + -
85C VAL* 4.3 9.9 - - + -
86C ARG 3.0 6.9 + - - +
87C GLY* 3.4 3.7 - - - -
88C LEU* 2.8 27.0 + - - +
114C VAL* 4.2 3.6 - - + -
115C PHE* 1.3 76.2 - - - +
117C ILE* 1.3 63.1 - - - +
112F GLU* 4.0 9.4 - - - +
113F THR 3.8 8.3 - - - +
114F VAL* 3.5 32.5 - - + -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.5 1.6 - - - -
22C ARG* 2.7 35.1 + - - +
88C LEU* 3.7 15.9 - - + +
116C LEU* 1.3 74.3 - - - +
118C ALA* 1.3 75.3 + - - +
98F LEU* 3.2 43.1 - - + +
101F ALA* 3.7 16.6 - - + -
102F LEU* 3.9 26.1 - - + +
113F THR* 4.4 5.1 + - - +
115F PHE* 3.3 38.4 - - + -
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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