Contacts of the strand formed by residues 279 - 284 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188L VAL* 5.9 0.9 - - - +
200L LEU* 3.4 36.1 - - + +
216L TRP* 3.7 31.6 - - + -
217L ILE 3.3 16.6 - - - +
218L GLU* 3.9 2.8 - - + +
237L TRP* 4.3 10.5 - - + +
269L VAL* 4.7 7.2 - - + -
271L THR* 4.8 1.8 - - + +
275L MET* 3.2 30.5 - - + -
278L GLN* 1.3 91.8 - - + +
280L VAL* 1.3 59.3 + - - +
294L THR* 5.8 0.9 - - - -
296L SER* 5.3 0.2 + - - -
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Residues in contact with VAL 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L VAL* 6.3 0.4 - - - -
215L LYS 3.6 0.7 - - - +
216L TRP* 3.6 7.3 - - - -
217L ILE* 2.8 38.2 + - + +
219L SER* 4.6 11.0 - - - +
222L PHE* 3.5 30.3 - - + -
226L TYR* 4.4 1.6 - - + -
279L PRO* 1.3 74.7 - - - +
281L CYS* 1.3 60.0 + - - +
282L VAL* 3.7 1.5 + - + -
292L VAL* 3.2 23.1 - - + -
293L TYR 2.7 24.5 - - - +
294L THR* 3.2 28.5 - - + +
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Residues in contact with CYS 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L VAL* 3.7 16.3 - - + +
202L CYS* 2.0 49.6 - - - -
214L THR* 3.3 20.4 - - - -
215L LYS 3.9 2.2 - - - -
216L TRP* 3.8 19.1 - - + -
280L VAL* 1.3 72.1 - - - +
282L VAL* 1.3 58.6 + - - +
283L VAL* 4.0 5.4 - - - -
292L VAL* 3.4 1.3 - - - -
293L TYR* 2.6 44.7 + - + +
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Residues in contact with VAL 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L THR* 3.4 5.1 + - - -
215L LYS* 2.8 52.3 + - + +
217L ILE* 3.9 23.3 - - + -
222L PHE* 4.0 17.7 - - + -
228L TYR* 3.9 20.0 - - + -
280L VAL 4.3 3.8 - - - +
281L CYS* 1.3 75.8 - - - +
283L VAL* 1.3 64.2 + - - +
284L PHE* 3.7 28.2 - - + -
290L ALA* 4.7 3.6 - - + -
291L GLN 3.3 12.3 - - - +
292L VAL* 4.2 7.2 - - + -
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Residues in contact with VAL 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L PRO* 5.3 0.9 - - + -
186L VAL* 4.2 5.2 - - + -
202L CYS* 4.1 2.0 - - - -
204L VAL* 4.0 34.8 - - + -
212L VAL* 4.6 5.8 - - + -
213L ILE 3.8 4.7 - - - +
214L THR* 4.1 4.5 - - - +
281L CYS* 4.0 20.4 - - - -
282L VAL* 1.3 75.1 - - - +
284L PHE* 1.3 68.5 + - - +
285L HIS* 4.6 5.2 - - + -
288L LEU* 3.6 19.6 - - + +
290L ALA* 3.4 4.3 - - - -
291L GLN 2.9 29.5 + - - -
293L TYR* 4.0 24.0 - - + -
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Residues in contact with PHE 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L THR* 3.3 19.2 - - - +
102L LEU* 4.3 9.4 - - + -
103L LEU* 3.5 37.7 - - + -
212L VAL* 3.6 3.6 - - - +
213L ILE* 2.8 43.4 + - + +
215L LYS* 3.4 35.2 - - + -
228L TYR* 3.7 34.3 - + - -
282L VAL* 3.7 24.5 - - + -
283L VAL* 1.3 71.8 - - - +
285L HIS* 1.3 63.8 + - - +
289L GLU 3.8 7.2 - - - +
290L ALA* 3.6 26.5 - - + -
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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