Contacts of the strand formed by residues 113 - 117 (chain F) in PDB entry 4WFH
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 THR 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F ALA 3.3 3.7 + - - -
112F PRO* 1.3 70.5 - - - +
114F VAL* 1.3 63.8 + - - +
115F SER* 5.1 3.6 + - - +
134F PHE 3.3 4.2 - - - +
136F ASN* 2.9 49.1 + - - +
137F ASN* 5.0 4.7 + - - +
140G THR* 5.1 10.1 - - - +
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Residues in contact with VAL 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PRO* 3.6 27.0 + - + +
113F THR* 1.3 78.2 - - - +
115F SER* 1.3 70.0 + - - +
133F CYS* 3.7 24.5 - - - -
134F PHE 3.3 4.5 - - - +
135F LEU* 4.3 11.7 - - + -
193F CYS* 4.5 5.4 - - - +
195F ALA* 4.3 7.6 - - + -
204F ILE* 3.9 23.3 - - + +
206F LYS* 3.2 47.6 + - + +
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Residues in contact with SER 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F THR* 5.1 4.6 + - - +
114F VAL* 1.3 79.2 + - - +
116F ILE* 1.3 61.7 + - - +
117F PHE* 3.9 26.9 - - - -
132F VAL 3.9 0.2 - - - +
133F CYS* 3.1 7.9 - - - -
134F PHE* 2.8 40.7 + - - -
206F LYS* 4.6 2.0 - - - -
140G THR* 3.7 22.5 + - - -
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F SER* 1.3 75.2 - - - +
117F PHE* 1.3 73.0 + - - +
118F PRO* 4.2 3.7 - - - +
131F VAL* 4.2 4.0 - - + -
132F VAL 3.4 7.9 - - - +
133F CYS* 4.3 4.0 - - - +
147F TRP* 3.7 27.4 - - + -
191F TYR 3.6 23.6 - - - +
193F CYS* 4.0 4.7 - - + +
206F LYS* 3.9 31.8 - - + +
207F SER 3.9 18.6 - - - +
208F PHE* 3.7 24.0 - - + -
129G PRO* 4.5 8.3 - - - +
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Residues in contact with PHE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F SER* 3.9 21.1 - - - -
116F ILE* 1.3 78.6 - - - +
118F PRO* 1.3 68.2 - - + +
130F SER 4.3 0.7 - - - +
131F VAL* 3.3 10.6 - - - +
132F VAL* 2.7 49.1 + - + +
134F PHE* 3.6 27.8 - + - -
208F PHE* 4.2 1.6 - - - -
127G LEU* 3.5 44.6 - - + -
128G ALA 3.5 19.7 - - - +
129G PRO* 3.8 11.9 - - + -
140G THR* 3.2 35.0 - - + -
141G LEU* 4.1 6.7 - - - -
142G GLY 4.4 0.2 - - - -
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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