Contacts of the strand formed by residues 111 - 116 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107L HIS* 4.7 9.2 - - + -
109L SER 4.4 2.2 - - - +
110L PRO* 1.3 79.3 - - - +
112L THR* 1.3 58.6 + - - +
113L ARG 3.9 14.4 - - - +
125L SER* 4.4 12.1 - - - -
126L ALA 3.2 18.2 - - - +
127L SER* 4.1 0.7 - - - +
384L THR* 3.0 27.1 + - - +
398L GLY* 4.2 13.9 - - - -
399L SER 3.3 25.3 + - - +
402L GLN* 3.8 16.6 - - - +
403L THR 3.6 17.3 - - - +
404L VAL* 4.2 8.7 - - + -
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Residues in contact with THR 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L VAL* 1.3 73.7 - - - +
113L ARG* 1.3 78.4 + - - +
126L ALA* 2.7 9.5 + - - -
127L SER* 2.9 21.3 - - - -
128L GLU* 3.9 10.0 + - + +
152L SER* 6.4 0.2 - - - -
153L VAL 2.6 29.2 + - - +
154L GLN* 3.6 33.7 - - + +
384L THR* 4.1 12.0 - - + +
385L SER* 3.2 10.8 + - - -
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Residues in contact with ARG 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L VAL* 3.8 4.4 - - - +
112L THR* 1.3 97.6 + - - +
114L VAL* 1.3 74.1 + - - +
115L ILE* 5.9 0.7 - - + -
125L SER* 3.4 4.2 - - - -
126L ALA* 3.1 28.2 + - + +
154L GLN* 2.6 33.0 + - - +
155L ASP* 2.8 36.7 + - - +
156L ILE* 4.6 15.3 - - + +
196L SER* 3.5 19.0 + - - -
197L SER* 4.8 0.8 + - - -
238L ARG 5.4 1.6 + - - -
239L MET* 4.2 12.4 - - - +
241L ARG* 3.5 16.7 - - - +
384L THR 4.8 2.1 + - - -
385L SER* 3.5 19.7 + - - -
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Residues in contact with VAL 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L VAL* 5.1 0.4 - - + -
113L ARG* 1.3 87.2 - - - +
115L ILE* 1.3 71.7 + - - +
123L MET* 3.5 17.9 - - + -
124L VAL 3.5 3.4 - - - +
125L SER* 4.5 1.3 - - - -
385L SER* 3.7 21.3 - - - +
386L LEU 4.0 6.4 - - - +
387L ASP* 4.1 11.0 - - - +
396L VAL* 3.9 18.6 - - + +
397L THR* 4.0 2.2 - - - -
398L GLY* 3.4 29.4 - - - +
404L VAL* 3.3 29.8 - - + -
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Residues in contact with ILE 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L ARG* 5.9 1.1 - - + -
114L VAL* 1.3 79.6 - - - +
116L PHE* 1.3 67.0 + - - +
123L MET* 3.1 7.2 - - - +
124L VAL* 2.8 61.3 + - + +
156L ILE* 3.3 39.0 - - + +
157L SER* 3.6 15.5 - - - -
158L PHE* 3.5 28.7 - - + +
387L ASP* 4.1 8.9 - - - +
396L VAL* 4.9 0.4 - - - +
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Residues in contact with PHE 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L ILE* 1.3 80.6 - - - +
117L HIS* 1.3 68.1 + - - +
118L PRO* 3.8 2.9 - - - +
122L VAL 4.2 0.7 - - - -
123L MET* 4.0 5.8 - - + -
137L TYR* 3.2 46.9 - + + -
158L PHE* 3.9 10.6 - - - +
387L ASP* 3.0 56.5 + - + +
388L PHE 3.8 9.0 - - - +
389L HIS* 3.8 27.8 - - + -
394L TYR* 3.7 20.9 - - + -
396L VAL* 3.3 26.5 - - + -
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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