Contacts of the strand formed by residues 248 - 253 (chain K) in PDB entry 1VYH
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 248 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K MET* 5.0 0.2 - - - +
241K ARG 4.6 0.2 - - - -
242K PRO* 3.5 5.5 - - - +
243K ASN* 3.1 50.4 + - + +
246K GLY 3.3 4.2 - - - +
247K THR* 1.3 91.7 - - + +
249K ILE* 1.3 64.0 + - - +
260K VAL* 4.3 20.9 - - + -
261K TRP 3.4 14.6 - - - +
262K VAL* 3.8 24.2 - - + -
263K VAL* 4.4 2.9 - - - +
269K LYS* 4.8 7.4 - - + -
284K TRP* 4.6 7.9 - - + -
309K PRO* 5.4 11.9 - - + -
325K VAL* 5.9 1.8 - - + -
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Residues in contact with ILE 249 (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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201K MET* 4.1 8.7 - - - -
208K VAL* 3.8 38.6 - - + -
216K ILE* 5.3 7.4 - - + -
230K PHE* 4.6 15.0 - - + -
240K VAL* 4.5 5.6 - - + -
241K ARG* 3.4 30.5 - - - +
242K PRO* 3.6 11.2 - - + -
248K LEU* 1.3 75.9 - - - +
250K ALA* 1.3 59.5 + - - +
260K VAL* 3.0 5.4 - - - -
261K TRP* 2.6 73.7 + - + +
263K VAL* 5.1 8.7 - - + +
284K TRP* 4.2 3.4 - - - -
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Residues in contact with ALA 250 (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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240K VAL* 3.1 9.1 - - - -
241K ARG* 2.8 36.5 + - + +
249K ILE* 1.3 71.7 - - - +
251K SER* 1.3 60.2 + - - +
259K ARG 3.4 4.5 - - - -
260K VAL* 4.1 0.7 - - - -
282K ILE* 3.1 18.3 - - + +
284K TRP* 3.4 30.2 - - + +
311K LEU* 3.5 21.3 - - + -
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Residues in contact with SER 251 (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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216K ILE* 3.5 16.4 - - - -
233K HIS* 2.8 32.5 + - - -
237K VAL* 4.0 1.6 - - - -
239K MET 3.3 8.1 - - - -
240K VAL* 4.3 1.6 - - - -
249K ILE 4.1 0.6 + - - -
250K ALA* 1.3 74.3 - - - +
252K CYS* 1.3 64.4 + - - +
258K VAL* 3.4 13.3 - - - +
259K ARG* 2.7 29.0 + - - +
261K TRP* 2.8 24.6 + - - -
282K ILE* 4.6 1.3 - - - +
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Residues in contact with CYS 252 (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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233K HIS* 4.1 0.6 + - - -
237K VAL* 3.0 5.0 - - - +
238K ARG* 2.5 35.5 + - - -
239K MET* 3.2 22.0 + - + +
251K SER* 1.3 80.0 + - - +
253K SER* 1.3 57.8 + - - +
257K THR 3.9 5.6 - - - -
258K VAL* 4.9 0.9 - - - +
279K VAL* 3.1 44.2 - - - -
280K GLU* 3.6 4.0 - - - -
281K CYS 3.4 25.8 - - - -
282K ILE* 3.8 8.5 - - + -
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Residues in contact with SER 253 (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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233K HIS* 2.6 29.1 - - - -
235K GLU 4.1 1.1 - - - -
236K TRP 2.8 22.4 - - - -
237K VAL* 3.8 2.5 - - - -
238K ARG* 4.1 5.2 - - - +
252K CYS* 1.3 79.9 - - - +
254K ASN* 1.3 60.9 + - - +
255K ASP* 2.1 29.2 + - - -
256K GLN 3.4 6.4 + - - -
257K THR 3.5 6.7 + - - -
278K VAL* 4.1 0.9 - - - -
279K VAL* 3.2 29.6 + - - +
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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