Contacts of the strand formed by residues 264 - 267 (chain C) in PDB entry 1TKK
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 LEU 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C LEU* 4.1 8.3 - - + -
240C PRO* 4.0 23.6 - - + -
241C ILE 3.2 2.6 + - - +
242C MET* 3.8 32.3 - - + -
243C ALA 2.9 23.0 + - - -
262C ALA* 3.4 6.3 - - - +
263C ASP* 1.3 93.3 - - + +
265C ILE* 1.3 68.0 + - - +
290C VAL* 3.9 2.2 - - - +
291C GLU* 3.4 33.4 - - + +
292C CYS 5.8 0.4 - - - -
319C ARG* 3.3 34.5 - - - +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C MET* 3.8 4.0 - - - -
243C ALA* 3.6 13.7 - - + +
247C VAL* 4.1 23.8 - - + -
253C ALA* 4.5 15.9 - - + -
256C VAL* 5.0 7.4 - - + -
257C LEU* 3.9 32.3 - - + -
262C ALA* 5.8 0.2 - - + -
264C LEU* 1.3 80.8 - - - +
266C ASN* 1.3 69.2 + - - +
267C ILE* 4.1 2.7 - - + -
281C ILE* 4.1 14.4 - - + -
285C ALA* 4.3 13.7 - - + -
290C VAL* 4.2 5.2 - - + -
291C GLU 3.3 5.9 + - - -
292C CYS* 3.1 14.8 - - - +
293C MET 2.8 30.8 + - - +
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Residues in contact with ASN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LYS* 4.3 0.4 - - - +
219C GLU* 3.1 25.5 + - - -
242C MET* 3.6 15.8 - - - +
243C ALA 2.8 17.7 + - - +
244C ASP* 3.4 15.8 + - + -
247C VAL* 4.1 0.7 - - - +
265C ILE* 1.3 78.6 - - - +
267C ILE* 1.3 73.2 + - - +
268C LYS* 3.4 24.7 + - - +
271C LYS* 2.8 25.8 + - - -
293C MET* 3.3 18.1 - - - +
295C GLY 4.0 6.4 + - - +
321C ASP* 4.9 1.8 + - - -
1603C MG 4.0 0.4 - - - -
2475C GLU 4.0 4.2 + - - -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C VAL 5.7 0.4 - - - -
265C ILE* 4.1 6.1 - - + -
266C ASN* 1.3 75.7 - - - +
268C LYS* 1.3 67.3 + - - +
269C LEU* 5.3 0.4 - - + -
271C LYS* 4.7 0.9 - - - +
272C ALA* 5.2 0.2 - - + -
278C ALA* 3.6 48.5 - - + +
281C ILE* 3.9 22.7 - - + -
282C ASN* 3.8 15.5 - - + +
292C CYS* 3.8 29.6 - - + -
293C MET 2.7 13.9 + - - +
294C VAL* 3.2 14.3 - - + +
295C GLY 3.0 25.3 + - - -
310C PHE* 4.2 11.9 - - + -
317C ILE* 4.8 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