Contacts of the strand formed by residues 248 - 253 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C PRO* 3.5 0.3 - - - +
243C ASN* 2.9 42.5 + - + +
246C GLY 3.3 1.7 - - - +
247C THR* 1.3 91.3 - - + +
249C ILE* 1.3 75.0 + - - +
260C VAL* 3.9 20.6 - - + -
261C TRP 3.2 18.6 - - - +
262C VAL* 3.6 22.7 - - + -
263C VAL* 4.4 1.3 - - - +
269C LYS* 5.0 11.0 - - + +
284C TRP* 4.1 15.5 - - + -
309C PRO* 5.7 9.0 - - + -
325C VAL* 6.2 0.7 - - + -
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Residues in contact with ILE 249 (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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201C MET* 4.0 25.8 - - + -
208C VAL* 4.1 21.1 - - + -
216C ILE* 5.2 2.9 - - + -
230C PHE* 4.9 14.4 - - + -
240C VAL* 4.5 11.9 - - + -
241C ARG 3.5 6.3 - - - +
242C PRO* 3.6 21.1 - - + -
248C LEU* 1.3 86.1 - - - +
250C ALA* 1.3 58.0 + - - +
260C VAL* 3.2 4.8 - - - -
261C TRP* 2.6 77.3 + - + +
263C VAL* 4.6 13.2 - - + -
284C TRP* 4.3 2.9 - - - -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL* 3.2 7.6 - - - -
241C ARG* 2.8 32.9 + - + +
249C ILE* 1.3 71.6 - - - +
251C SER* 1.3 61.6 + - - +
259C ARG 3.4 4.9 - - - -
260C VAL* 4.2 1.3 - - + -
282C ILE* 3.3 15.3 - - + +
284C TRP* 3.6 26.7 - - + +
311C LEU* 3.6 26.9 - - + -
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Residues in contact with SER 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 3.5 18.2 - - - -
233C HIS* 2.5 34.8 + - - -
237C VAL* 4.5 1.1 - - - -
239C MET 3.3 8.7 - - - -
240C VAL* 4.5 2.2 - - - -
249C ILE 4.0 0.6 + - - -
250C ALA* 1.3 72.8 - - - +
252C CYS* 1.3 61.3 + - - +
258C VAL* 3.2 13.9 - - - +
259C ARG* 2.7 27.6 + - - +
261C TRP* 3.2 24.2 + - - -
282C ILE* 3.2 1.4 - - - +
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Residues in contact with CYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C HIS* 4.1 0.8 + - - -
237C VAL* 3.5 2.1 - - - +
238C ARG* 2.6 35.6 + - - -
239C MET* 3.4 21.9 + - + +
251C SER* 1.3 80.4 + - - +
253C SER* 1.3 56.2 + - - +
257C THR 3.8 7.2 - - - -
258C VAL* 4.6 2.5 - - + -
279C VAL* 3.4 24.2 - - - -
280C GLU 3.6 4.3 - - - -
281C CYS 3.5 24.2 - - - -
282C ILE* 3.2 23.1 - - + -
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Residues in contact with SER 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C HIS* 2.5 30.1 - - - -
236C TRP 2.8 19.7 - - - -
237C VAL* 3.9 1.8 - - - -
238C ARG* 4.0 5.2 - - - -
252C CYS* 1.3 77.5 - - - +
254C ASN* 1.3 65.7 + - - +
255C ASP* 2.4 24.6 + - - -
256C GLN 3.4 6.3 + - - -
257C THR 3.4 8.8 + - - -
278C VAL* 3.9 4.9 - - - -
279C VAL* 3.2 25.9 + - - +
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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