Contacts of the strand formed by residues 113 - 117 (chain F) in PDB entry 3KYM
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLU* 4.3 6.4 - - - +
7F SER* 4.0 26.5 + - - +
9F GLY* 3.7 30.8 + - - +
20F LEU* 4.4 14.9 - - - +
36F TRP* 5.7 1.2 - - - -
93F THR* 2.9 8.5 - - - -
94F TYR* 2.9 34.4 + - - +
112F GLY* 1.3 80.2 - - - +
114F LEU* 1.3 62.7 + - - +
115F VAL* 3.5 2.6 + - - +
57J ILE* 5.9 3.1 - - + -
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Residues in contact with LEU 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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9F GLY* 3.5 1.0 - - - -
10F GLY* 2.9 26.3 + - - -
41F PRO* 5.7 5.4 - - + -
91F THR* 5.5 4.3 - - + -
92F ALA* 3.8 11.7 - - - +
93F THR* 3.7 24.0 - - + +
113F THR* 1.3 74.6 - - - +
115F VAL* 1.3 64.1 + - - +
116F THR* 3.4 22.5 + - + +
154F GLU* 3.9 37.2 - - + +
155F PRO* 5.7 2.5 - - + -
182F TYR* 6.1 0.4 - - - +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLY* 4.6 4.5 - - - -
10F GLY 4.0 5.4 - - - +
12F VAL* 4.9 7.4 - - + -
18F LEU* 5.0 2.7 - - + -
20F LEU* 3.8 28.9 - - + -
83F MET* 4.1 13.7 - - + -
86F LEU* 4.9 6.7 - - + -
90F ASP 4.3 4.5 - - - +
91F THR* 3.6 5.9 - - - +
92F ALA 2.8 31.3 + - - +
94F TYR* 3.5 36.6 - - + -
113F THR 3.5 1.7 + - - +
114F LEU* 1.3 76.9 - - - +
116F THR* 1.3 61.1 + - - +
117F VAL* 4.2 19.7 - - + -
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F GLY* 3.3 12.6 + - - +
11F LEU* 3.4 21.0 - - + +
12F VAL* 2.9 27.4 + - - +
91F THR* 4.3 9.9 - - + -
114F LEU* 3.4 29.0 + - + +
115F VAL* 1.3 75.6 - - - +
117F VAL* 1.3 64.4 + - - +
118F SER* 5.1 0.7 - - - -
152F PHE* 4.5 14.4 - - + -
153F PRO* 4.8 10.0 - - + +
154F GLU* 5.6 1.2 + - + +
182F TYR* 5.0 11.9 - - + +
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Residues in contact with VAL 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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12F VAL* 3.3 6.3 - - + +
14F PRO* 4.0 26.9 - - + +
86F LEU* 4.0 23.3 - - + +
87F ARG 3.4 35.4 - - - +
88F ALA* 3.5 13.0 - - - +
90F ASP* 4.6 2.5 - - + -
91F THR* 3.2 26.8 + - - +
115F VAL* 4.3 17.0 - - + -
116F THR* 1.3 75.0 - - - +
118F SER* 1.3 64.6 + - - +
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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