Contacts of the strand formed by residues 248 - 253 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S MET* 5.0 0.2 - - - +
242S PRO* 3.5 4.9 - - - +
243S ASN* 3.0 51.5 + - + +
246S GLY 3.3 3.6 - - - +
247S THR* 1.3 86.9 - - - +
249S ILE* 1.3 63.4 + - - +
260S VAL* 4.2 13.9 - - + -
261S TRP 3.4 17.9 - - - +
262S VAL* 3.9 25.1 - - + -
263S VAL* 4.4 2.7 - - - +
269S LYS* 5.1 7.6 - - + -
284S TRP* 4.1 15.3 - - + -
309S PRO* 5.7 8.1 - - + -
325S VAL* 6.4 0.9 - - + -
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Residues in contact with ILE 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201S MET* 4.5 6.5 - - + -
208S VAL* 3.8 39.5 - - + -
216S ILE* 5.5 1.1 - - + -
230S PHE* 4.8 16.6 - - + -
240S VAL* 4.4 9.2 - - + -
241S ARG 3.4 28.9 - - - +
242S PRO* 3.7 11.4 - - + -
248S LEU* 1.3 75.3 - - - +
250S ALA* 1.3 60.0 + - - +
259S ARG 3.6 0.7 - - - +
260S VAL* 3.1 5.0 - - - +
261S TRP* 2.6 76.6 + - + +
263S VAL* 5.2 8.7 - - + +
284S TRP* 4.2 4.0 - - - -
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Residues in contact with ALA 250 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240S VAL* 3.1 8.4 - - - -
241S ARG* 2.8 36.7 + - + +
249S ILE* 1.3 71.7 - - - +
251S SER* 1.3 60.3 + - - +
259S ARG 3.3 5.6 - - - +
260S VAL* 4.5 8.1 - - + +
282S ILE* 3.3 20.6 - - + +
284S TRP* 3.7 29.8 - - + +
311S LEU* 4.6 10.1 - - + -
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Residues in contact with SER 251 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216S ILE* 3.6 19.3 - - - -
233S HIS* 2.8 27.4 + - - -
237S VAL* 4.2 0.2 - - - -
239S MET 3.3 5.8 - - - -
240S VAL* 4.4 1.3 - - - -
249S ILE 4.1 0.4 + - - -
250S ALA* 1.3 74.0 - - - +
252S CYS* 1.3 62.2 + - - +
258S VAL* 3.3 14.7 - - - +
259S ARG* 2.7 43.8 + - - +
261S TRP* 3.1 17.2 + - - -
282S ILE* 3.3 2.8 - - - +
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Residues in contact with CYS 252 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233S HIS* 4.2 0.4 + - - -
237S VAL* 3.2 5.2 - - - +
238S ARG* 2.4 36.3 + - + -
239S MET* 3.2 19.1 + - + +
251S SER* 1.3 76.5 - - - +
253S SER* 1.3 57.9 + - - +
257S THR 3.9 4.0 - - - -
258S VAL* 4.1 4.0 - - - -
279S VAL* 3.6 23.3 - - - -
281S CYS 3.3 40.4 - - - -
282S ILE* 3.4 18.8 - - + -
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Residues in contact with SER 253 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233S HIS* 2.8 30.3 - - - -
235S GLU 4.2 0.2 - - - -
236S TRP 3.1 15.3 - - - -
237S VAL* 4.1 1.3 - - - -
238S ARG 4.1 2.0 - - - +
252S CYS* 1.3 76.9 - - - +
254S ASN* 1.3 68.0 + - - +
255S ASP* 2.4 26.4 + - - -
256S GLN 3.4 6.2 + - - -
257S THR 3.1 11.0 + - - -
279S VAL* 3.3 31.6 + - - +
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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