Contacts of the strand formed by residues 210 - 214 (chain F) in PDB entry 1KR2
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 ILE 210 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LEU* 5.0 5.6 - - + -
178F VAL* 3.9 31.0 - - + -
183F LEU* 3.4 23.8 - - + +
185F CYS* 5.2 3.1 - - + -
197F ILE* 3.5 30.7 - - + +
203F LEU* 3.8 40.2 - - + +
206F HIS 3.7 7.9 - - - +
207F ARG* 3.0 16.8 + - - +
208F SER 3.4 0.4 - - - -
209F ASN* 1.3 83.3 - - - +
211F HIS* 1.3 62.6 + - - +
212F VAL* 3.6 10.2 + - + +
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Residues in contact with HIS 211 (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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34F TYR* 3.9 32.2 + + + +
35F MET* 4.2 20.2 - - + -
38F THR* 6.3 0.9 - - + -
40F ARG* 5.1 9.9 - - - -
41F TYR* 3.4 35.0 + + - -
152F LYS* 5.1 4.6 + - + -
183F LEU 2.8 16.8 + - - +
184F ILE* 3.4 9.9 - - + -
185F CYS* 2.8 27.9 + - - -
208F SER 3.6 22.0 + - - -
209F ASN* 4.2 14.4 + - - -
210F ILE* 1.3 71.3 + - - +
212F VAL* 1.3 61.8 + - - +
213F VAL* 3.6 2.6 + - - +
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Residues in contact with VAL 212 (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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34F TYR* 4.5 11.7 + - - -
185F CYS* 3.4 13.2 - - + +
187F THR* 4.1 20.2 - - + -
190F GLY* 4.3 12.6 - - - +
193F ALA* 4.3 11.9 - - + -
194F GLN* 4.1 22.2 - - + +
197F ILE* 3.8 28.7 - - + -
210F ILE* 3.6 7.2 + - + +
211F HIS* 1.3 72.1 - - - +
213F VAL* 1.3 61.8 + - - +
214F ASN* 3.8 16.9 + - - +
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Residues in contact with VAL 213 (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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30F LEU* 4.1 20.6 - - + +
31F ALA* 4.8 1.3 - - - -
34F TYR* 3.6 50.7 - - + -
184F ILE* 3.9 24.0 - - + -
185F CYS 2.8 10.0 + - - +
186F VAL* 3.3 18.0 - - + +
187F THR 3.0 24.8 + - - +
211F HIS 4.0 3.4 - - - +
212F VAL* 1.3 74.0 - - - +
214F ASN* 1.3 71.4 + - - +
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Residues in contact with ASN 214 (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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191D ASN* 4.2 6.6 + - - +
194D GLN* 3.8 26.4 + - - +
30F LEU* 4.5 5.4 - - - +
34F TYR* 5.9 0.2 - - - -
187F THR* 3.4 6.7 - - - +
190F GLY* 4.0 21.5 - - - -
212F VAL* 3.8 10.5 + - - +
213F VAL* 1.3 85.7 - - - +
215F GLU* 1.3 60.9 + - - +
216F TRP* 3.6 46.0 + - + +
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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