Contacts of the strand formed by residues 111 - 116 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G HIS* 4.0 21.8 - - + -
110G PRO* 1.3 76.8 - - - +
112G THR* 1.3 62.6 + - - +
113G ARG 3.9 13.5 - - - +
114G VAL* 4.3 7.6 - - + -
125G SER* 4.3 4.7 - - - +
126G ALA 3.4 12.8 - - - +
127G SER* 3.9 0.4 - - - -
384G THR* 3.2 25.5 + - - +
398G GLY* 4.5 2.9 - - - -
399G SER 3.0 18.0 + - - +
400G VAL* 5.1 0.3 - - - +
402G GLN* 3.9 16.2 - - - -
403G THR 3.7 19.1 - - - +
404G VAL* 3.9 20.9 - - + -
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Residues in contact with THR 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G PRO 3.9 0.9 + - - -
111G VAL* 1.3 74.6 - - - +
113G ARG* 1.3 81.2 + - - +
126G ALA* 2.7 11.4 + - - -
127G SER* 3.2 17.2 - - - -
128G GLU* 3.7 10.7 + - + +
153G VAL 3.0 25.3 + - - +
154G GLN* 3.5 35.4 - - + +
384G THR* 4.3 13.8 - - + +
385G SER* 3.5 8.6 + - - -
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Residues in contact with ARG 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G VAL* 3.9 1.4 - - - +
112G THR* 1.3 96.3 + - - +
114G VAL* 1.3 72.0 + - - +
115G ILE* 5.4 3.1 - - + -
125G SER* 3.4 4.7 - - - -
126G ALA* 3.1 25.9 + - + +
154G GLN* 2.9 25.1 + - - +
155G ASP* 2.6 39.8 + - - +
156G ILE* 3.7 24.0 - - + +
196G SER* 3.7 16.6 + - - -
238G ARG 5.4 1.8 + - - -
239G MET* 4.2 13.3 - - - +
241G ARG* 3.7 14.5 - - - +
384G THR 4.9 2.4 + - - -
385G SER* 3.1 17.9 + - - -
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Residues in contact with VAL 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G VAL* 4.3 7.6 - - + -
113G ARG* 1.3 86.0 - - - +
115G ILE* 1.3 71.8 + - - +
123G MET* 3.7 19.3 - - + -
124G VAL 3.5 10.8 - - - +
125G SER* 4.7 1.1 - - - -
385G SER* 3.4 20.8 + - - +
386G LEU 4.6 5.1 - - - +
387G ASP* 4.0 14.0 - - - +
396G VAL* 3.6 34.1 - - + +
397G THR 4.1 2.2 - - - +
398G GLY* 3.8 27.1 - - - +
404G VAL* 4.5 5.8 - - + -
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Residues in contact with ILE 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G ARG* 5.4 4.0 - - + -
114G VAL* 1.3 80.2 - - - +
116G PHE* 1.3 65.1 + - - +
123G MET* 3.2 8.4 - - - +
124G VAL* 2.8 57.7 + - + +
156G ILE* 3.0 50.9 - - + +
157G SER* 4.0 8.1 - - - -
158G PHE* 4.0 23.3 - - + +
387G ASP* 3.9 14.6 - - - +
396G VAL* 5.1 0.2 - - - -
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Residues in contact with PHE 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G ILE* 1.3 79.8 - - - +
117G HIS* 1.3 66.1 + - - +
118G PRO* 3.7 3.5 - - - +
122G VAL 4.2 0.7 - - - -
123G MET* 3.7 7.2 - - + -
137G TYR* 3.4 45.3 - + + -
158G PHE* 3.5 14.1 - - - +
387G ASP* 3.6 32.7 + - + +
388G PHE 3.9 4.5 - - - -
389G HIS* 3.4 49.8 - + + -
394G TYR* 3.5 24.7 - - + -
396G VAL* 3.7 27.8 - - + -
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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