Contacts of the strand formed by residues 264 - 267 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D ARG* 6.4 2.2 - - - -
217F LEU* 3.8 13.5 - - + -
240F PRO* 4.1 18.2 - - + -
241F ILE 3.0 2.8 + - - +
242F MET* 3.7 35.2 - - + -
243F ALA 2.9 22.9 + - - -
262F ALA* 3.5 3.8 - - - +
263F ASP* 1.3 92.0 - - + +
265F ILE* 1.3 69.6 + - - +
290F VAL* 3.8 1.8 - - - -
291F GLU* 3.6 31.6 - - + +
319F ARG* 3.2 32.3 - - - +
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Residues in contact with ILE 265 (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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242F MET* 3.7 4.9 - - - +
243F ALA* 3.6 15.5 - - + +
247F VAL* 4.3 20.0 - - + -
253F ALA* 4.5 16.4 - - + -
256F VAL* 4.7 10.5 - - + -
257F LEU* 4.3 31.0 - - + -
262F ALA* 5.4 0.4 - - + -
264F LEU* 1.3 80.5 - - - +
266F ASN* 1.3 73.5 + - - +
267F ILE* 4.2 10.8 - - + -
281F ILE* 4.4 5.8 - - + -
285F ALA* 4.6 7.4 - - + -
290F VAL* 4.4 6.7 - - + -
291F GLU 3.3 7.1 + - - -
292F CYS* 3.1 14.8 - - - +
293F MET 2.7 31.7 + - - +
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Residues in contact with ASN 266 (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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160F LYS* 4.6 0.4 - - - +
219F GLU* 3.3 16.7 + - - +
242F MET* 3.6 15.8 - - - +
243F ALA 3.0 15.0 + - - +
244F ASP* 4.0 15.7 - - + -
247F VAL 4.0 3.1 - - - +
265F ILE* 1.3 82.8 - - - +
267F ILE* 1.3 63.7 + - - +
268F LYS* 3.4 35.4 - - - +
271F LYS* 3.1 23.4 + - - -
293F MET* 3.3 25.9 - - - +
295F GLY* 4.3 7.9 - - - +
321F ASP* 4.7 0.2 + - - -
2481F GLU 4.2 2.4 + - - -
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Residues in contact with ILE 267 (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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247F VAL 5.7 0.4 - - - -
265F ILE* 4.2 4.7 - - + -
266F ASN* 1.3 76.4 + - - +
268F LYS* 1.3 68.7 + - - +
269F LEU* 5.0 0.7 - - + +
271F LYS* 4.7 0.7 - - - +
272F ALA* 5.2 2.2 - - + -
278F ALA* 3.6 35.4 - - + +
281F ILE* 3.9 29.4 - - + -
282F ASN* 4.0 16.4 - - + +
292F CYS* 3.5 34.8 - - + -
293F MET 2.8 10.2 + - - +
294F VAL* 3.3 13.6 - - + +
295F GLY 3.1 24.1 + - - -
310F PHE* 4.2 12.1 - - + -
317F ILE* 5.0 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