Contacts of the strand formed by residues 279 - 284 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K LEU* 3.4 34.4 - - + +
216K TRP* 3.7 31.2 - - + -
217K ILE 3.3 16.4 - - - +
218K GLU* 3.9 2.1 - - - +
237K TRP* 4.3 10.5 - - + +
269K VAL* 4.7 7.4 - - + -
271K THR* 4.8 1.3 - - + +
275K MET* 3.2 30.1 - - + -
278K GLN* 1.3 93.6 - - + +
280K VAL* 1.3 59.1 + - - +
294K THR* 5.8 0.7 - - - -
296K SER* 5.3 0.2 + - - -
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Residues in contact with VAL 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K VAL* 6.3 0.4 - - - -
215K LYS 3.6 0.7 - - - +
216K TRP* 3.5 8.6 - - - -
217K ILE* 2.8 37.1 + - + +
219K SER* 4.6 11.7 - - - -
222K PHE* 3.5 30.7 - - + -
226K TYR* 4.4 2.2 - - + -
278K GLN 5.0 0.2 - - - +
279K PRO* 1.3 75.2 - - - +
281K CYS* 1.3 59.7 + - - +
282K VAL* 3.7 1.5 + - + +
292K VAL* 3.2 22.0 - - + -
293K TYR 2.8 24.5 - - - +
294K THR* 3.2 28.5 - - + +
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Residues in contact with CYS 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K VAL* 3.7 16.5 - - + +
202K CYS* 2.0 50.5 - - - -
214K THR* 3.3 21.1 - - - -
215K LYS 3.8 2.2 - - - -
216K TRP* 3.8 18.4 - - + -
280K VAL* 1.3 72.5 - - - +
282K VAL* 1.3 59.8 + - - +
283K VAL* 3.9 5.4 - - - -
292K VAL* 3.4 1.1 - - - -
293K TYR* 2.7 43.4 + - + +
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Residues in contact with VAL 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K THR* 3.4 5.1 + - - -
215K LYS* 2.8 52.8 + - + +
217K ILE* 3.9 24.5 - - + -
222K PHE* 4.0 17.7 - - + -
228K TYR* 3.9 19.5 - - + -
280K VAL 4.4 2.9 - - - +
281K CYS* 1.3 74.8 - - - +
283K VAL* 1.3 63.6 + - - +
284K PHE* 3.7 28.1 - - + -
290K ALA* 4.7 3.4 - - + -
291K GLN 3.3 11.9 - - - +
292K VAL* 4.2 7.2 - - + -
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Residues in contact with VAL 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184K PRO* 5.3 0.9 - - + -
186K VAL* 4.2 4.7 - - + -
202K CYS* 4.1 1.8 - - - -
204K VAL* 4.0 37.0 - - + -
212K VAL* 4.6 6.1 - - + -
213K ILE 3.8 5.2 - - - +
214K THR* 4.2 4.3 - - - +
281K CYS* 3.9 19.7 - - - -
282K VAL* 1.3 74.8 - - - +
284K PHE* 1.3 69.2 + - - +
285K HIS* 4.6 3.6 - - + -
288K LEU* 3.7 18.5 - - + +
290K ALA* 3.4 3.9 - - - -
291K GLN 2.8 30.4 + - - -
293K TYR* 4.0 24.5 - - + -
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Residues in contact with PHE 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K THR* 3.3 19.8 - - - +
102K LEU* 4.2 9.0 - - + -
103K LEU* 3.5 38.4 - - + -
212K VAL* 3.6 3.6 - - - +
213K ILE* 2.8 43.7 + - + +
215K LYS* 3.4 35.4 - - + -
228K TYR* 3.7 34.3 - + - -
282K VAL* 3.7 23.3 - - + -
283K VAL* 1.3 71.2 - - - +
285K HIS* 1.3 64.3 + - - +
289K GLU 3.8 6.7 - - - +
290K ALA* 3.6 25.1 - - + -
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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