Contacts of the strand formed by residues 279 - 284 (chain F) in PDB entry 3IT8
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 PRO 279 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F VAL* 6.0 0.7 - - - +
200F LEU* 3.4 33.5 - - + +
216F TRP* 3.7 31.5 - - + -
217F ILE 3.2 17.0 - - - +
218F GLU* 3.9 2.3 - - + -
237F TRP* 4.3 10.8 - - + +
269F VAL* 4.7 7.2 - - + -
271F THR* 4.8 1.6 - - + +
275F MET* 3.2 31.1 - - + -
278F GLN* 1.3 92.3 - - + +
280F VAL* 1.3 59.7 + - - +
294F THR* 5.8 0.9 - - - -
296F SER* 5.3 0.2 + - - -
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Residues in contact with VAL 280 (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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188F VAL* 6.3 0.4 - - - -
215F LYS 3.6 0.7 - - - +
216F TRP* 3.5 9.0 - - - -
217F ILE* 2.8 36.9 + - + +
219F SER* 4.6 11.0 - - - -
222F PHE* 3.5 30.5 - - + -
226F TYR* 4.4 2.0 - - + -
279F PRO* 1.3 74.5 - - - +
281F CYS* 1.3 59.5 + - - +
282F VAL* 3.7 1.3 + - + -
292F VAL* 3.2 22.2 - - + -
293F TYR 2.7 24.7 - - - +
294F THR* 3.1 28.5 - - + +
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Residues in contact with CYS 281 (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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188F VAL* 3.7 16.3 - - + +
202F CYS* 2.0 50.7 - - - -
214F THR* 3.3 20.0 - - - -
215F LYS 3.9 3.1 - - - -
216F TRP* 3.8 18.9 - - + -
280F VAL* 1.3 71.7 - - - +
282F VAL* 1.3 60.0 + - - +
283F VAL* 4.0 5.2 - - - -
292F VAL* 3.4 1.1 - - - -
293F TYR* 2.7 43.6 + - + +
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Residues in contact with VAL 282 (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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214F THR* 3.4 5.7 + - - -
215F LYS* 2.8 48.6 + - + +
217F ILE* 3.8 24.5 - - + -
222F PHE* 4.0 17.3 - - + -
228F TYR* 3.9 20.0 - - + -
280F VAL 4.4 3.6 - - - +
281F CYS* 1.3 74.4 - - - +
283F VAL* 1.3 62.5 + - - +
284F PHE* 3.7 31.2 - - + -
290F ALA* 4.7 3.4 - - + -
291F GLN 3.3 12.8 - - - +
292F VAL* 4.3 7.4 - - + -
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Residues in contact with VAL 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F PRO* 5.3 1.1 - - + -
186F VAL* 4.2 5.2 - - + -
202F CYS* 4.1 2.0 - - - -
204F VAL* 4.0 33.9 - - + -
212F VAL* 4.6 7.9 - - + -
213F ILE 3.8 4.7 - - - +
214F THR* 4.2 4.3 - - - +
281F CYS* 4.0 20.0 - - - -
282F VAL* 1.3 75.4 - - - +
284F PHE* 1.3 69.4 + - - +
285F HIS* 4.6 4.0 - - + -
288F LEU* 3.7 18.2 - - + +
290F ALA* 3.4 4.6 - - - -
291F GLN 2.9 30.3 + - - -
293F TYR* 4.0 24.7 - - + -
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Residues in contact with PHE 284 (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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100F THR* 3.3 19.6 - - - +
102F LEU* 4.2 9.4 - - + -
103F LEU* 3.5 39.3 - - + -
212F VAL* 3.6 3.6 - - - +
213F ILE* 2.8 42.2 + - + +
215F LYS* 3.5 33.9 - - + -
228F TYR* 3.7 33.0 - + - -
282F VAL* 3.7 25.1 - - + -
283F VAL* 1.3 72.0 - - - +
285F HIS* 1.3 63.5 + - - +
289F GLU 3.8 6.1 - - - -
290F ALA* 3.6 23.8 - - + -
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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