Contacts of the strand formed by residues 252 - 258 (chain C) in PDB entry 3F7F
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 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C ASN* 3.4 15.4 + - - +
246C TRP* 3.5 4.9 - - - -
247C ASP 3.2 11.9 + - - -
250C SER* 3.2 28.3 + - - -
251C PHE* 1.3 76.5 + - - +
253C LEU* 1.3 79.1 + - - +
254C ILE* 3.0 24.9 + - + +
187D LYS* 5.1 14.6 - - + -
197D LEU* 4.5 15.2 - - + +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ASN* 4.2 5.8 + - - +
203C SER* 4.9 10.8 - - - +
244C LYS* 3.7 26.7 - - + -
245C ILE 3.6 10.8 - - - +
246C TRP* 3.1 40.2 - - + -
252C THR* 1.3 80.7 - - - +
254C ILE* 1.3 60.3 + - - +
255C GLN 2.9 29.8 - - - +
256C ASP* 4.5 15.5 - - + +
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Residues in contact with ILE 254 (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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233C TYR* 5.5 1.3 - - + -
245C ILE* 2.8 15.8 + - + +
247C ASP* 3.1 41.1 - - + +
250C SER* 4.7 4.3 - - - +
252C THR* 3.1 26.0 - - + +
253C LEU* 1.3 76.8 - - - +
255C GLN* 1.3 81.2 + - + +
311C LEU* 4.7 17.5 - - + +
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Residues in contact with GLN 255 (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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244C LYS* 3.5 0.3 - - - -
245C ILE* 3.3 32.0 + - + -
253C LEU* 2.9 27.4 - - - +
254C ILE* 1.3 93.8 + - + +
256C ASP* 1.3 64.3 + - - +
257C TYR* 3.2 41.8 + - + +
311C LEU 2.7 27.0 - - - +
312C THR* 4.2 4.5 + - - +
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Residues in contact with ASP 256 (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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206C LYS* 4.9 8.5 + - - -
242C HIS* 3.4 24.8 + - - +
243C LEU 3.9 4.7 - - - -
244C LYS* 3.7 27.7 - - + +
253C LEU* 4.5 11.7 - - + +
255C GLN* 1.3 83.4 - - - +
257C TYR* 1.3 60.0 + - - +
258C ASP* 4.2 0.5 + - - +
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Residues in contact with TYR 257 (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 HIS* 3.2 12.4 + - - -
243C LEU* 3.0 42.2 + - + +
245C ILE* 3.9 5.2 - - + -
255C GLN* 3.2 50.7 + - + +
256C ASP* 1.3 75.1 - - - +
258C ASP* 1.3 60.5 + - - +
259C MET* 3.7 18.4 - - + -
312C THR* 3.6 5.9 - - + +
313C TYR* 2.7 63.4 + + + -
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Residues in contact with ASP 258 (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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560B ASN* 3.4 22.2 + - + +
240C ASN 4.6 1.0 - - - +
241C CYS 4.5 2.5 - - - +
242C HIS* 3.8 27.1 + - + -
256C ASP 4.2 0.6 + - - -
257C TYR* 1.3 73.8 - - - +
259C MET* 1.3 65.0 + - - +
260C VAL* 2.9 28.8 + - - +
261C SER* 3.2 34.1 + - - +
262C GLN* 4.4 5.9 + - - +
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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