Contacts of the strand formed by residues 111 - 116 (chain T) 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 VAL 111 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107T HIS* 4.8 10.3 - - + -
109T SER 4.6 2.0 - - - +
110T PRO* 1.3 77.5 - - - +
112T THR* 1.3 59.8 + - - +
113T ARG 3.9 13.9 - - - +
114T VAL* 4.6 0.2 - - + -
125T SER* 4.2 7.0 - - - +
126T ALA 3.3 16.8 - - - +
127T SER* 4.2 1.6 - - - -
384T THR* 3.7 21.1 - - - +
385T SER* 4.4 0.8 + - - +
398T GLY* 4.2 4.7 - - - -
399T SER 3.7 18.3 + - - +
402T GLN* 3.9 5.8 - - - -
403T THR 3.5 38.8 - - - +
404T VAL* 3.6 22.7 - - + -
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Residues in contact with THR 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T PRO 4.0 0.5 + - - -
111T VAL* 1.3 73.3 - - - +
113T ARG* 1.3 81.1 + - - +
126T ALA* 2.7 13.0 + - - -
127T SER* 3.4 14.7 - - - -
128T GLU* 3.8 10.7 + - + +
153T VAL 2.9 20.4 + - - +
154T GLN* 3.2 44.3 - - + +
342T ARG* 6.0 1.6 - - - +
384T THR* 3.9 11.4 - - + +
385T SER* 3.0 12.9 + - - -
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Residues in contact with ARG 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T VAL* 3.9 1.3 - - - +
112T THR* 1.3 100.1 + - - +
114T VAL* 1.3 68.3 + - - +
115T ILE* 4.5 10.8 - - + -
124T VAL 4.7 0.2 - - - -
125T SER* 3.3 5.2 - - - -
126T ALA* 3.0 36.8 + - + +
154T GLN* 3.3 26.5 + - - +
155T ASP* 2.9 40.1 + - - +
156T ILE* 4.2 11.8 - - + +
196T SER 4.3 10.5 + - - -
197T SER* 4.9 2.0 + - - -
238T ARG 5.8 1.0 + - - -
239T MET* 5.3 10.3 - - - +
241T ARG* 4.4 8.8 - - - +
342T ARG* 5.2 11.2 + - - +
384T THR 4.6 3.8 + - - -
385T SER* 3.2 17.3 + - - -
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Residues in contact with VAL 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T VAL* 4.6 0.7 - - + -
113T ARG* 1.3 81.0 - - - +
115T ILE* 1.3 76.2 + - - +
123T MET* 3.5 19.5 - - + -
124T VAL 3.5 2.5 - - - +
125T SER* 4.6 0.2 - - - -
385T SER* 3.5 22.1 - - - +
386T LEU 5.0 3.4 - - - +
387T ASP* 4.0 13.6 - - + +
396T VAL* 3.6 18.4 - - + +
397T THR* 3.8 1.3 - - - -
398T GLY* 3.3 34.1 - - - +
404T VAL* 3.4 31.0 - - + -
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Residues in contact with ILE 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ARG* 4.5 11.2 - - + -
114T VAL* 1.3 86.3 - - - +
116T PHE* 1.3 64.1 + - - +
123T MET* 2.9 9.7 - - - +
124T VAL* 2.7 46.2 + - + +
155T ASP* 5.1 0.7 - - - +
156T ILE* 3.4 50.7 - - + +
157T SER* 5.1 4.3 - - - -
158T PHE* 3.8 32.5 - - + +
241T ARG* 6.0 2.2 - - - +
387T ASP* 4.1 10.1 - - - +
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Residues in contact with PHE 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115T ILE* 1.3 79.4 - - - +
117T HIS* 1.3 63.5 + - - +
118T PRO* 3.7 3.1 - - - +
122T VAL 4.3 0.4 - - - -
123T MET* 3.8 5.4 - - + -
137T TYR* 3.5 49.4 - + - -
158T PHE* 3.7 11.1 - - - +
387T ASP* 3.0 53.1 + - - +
388T PHE 3.8 10.5 - - - +
389T HIS* 3.7 25.6 - + + -
394T TYR* 3.7 29.4 - - + -
396T VAL* 3.5 31.0 - - + -
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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