Contacts of the strand formed by residues 248 - 253 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H PRO* 3.4 4.2 - - - +
243H ASN* 3.1 44.2 + - + +
246H GLY 3.3 2.4 + - - +
247H THR* 1.3 88.4 - - + +
249H ILE* 1.3 67.4 + - - +
260H VAL* 4.3 14.4 - - + -
261H TRP 3.3 12.1 - - - +
262H VAL* 3.2 34.8 - - + -
263H VAL* 4.3 1.8 - - - +
269H LYS* 4.6 11.7 - - + -
284H TRP* 4.4 15.5 - - + -
309H PRO* 5.7 7.9 - - + -
325H VAL* 6.0 1.6 - - + -
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Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H MET* 3.9 21.5 - - + -
208H VAL* 3.7 38.4 - - + -
216H ILE* 5.1 4.0 - - + -
218H MET* 5.4 1.3 - - + -
230H PHE* 4.8 11.0 - - + -
240H VAL* 4.3 14.4 - - + -
241H ARG 3.4 18.2 - - - +
242H PRO* 4.4 0.4 - - + -
248H LEU* 1.3 75.9 - - - +
250H ALA* 1.3 58.9 + - - +
260H VAL* 3.1 5.1 - - - -
261H TRP* 2.6 70.5 + - + +
263H VAL* 4.2 15.0 - - + -
284H TRP* 4.3 2.9 - - - -
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Residues in contact with ALA 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H VAL* 3.1 6.2 - - - -
241H ARG* 2.7 37.6 + - + +
249H ILE* 1.3 74.9 - - - +
251H SER* 1.3 61.2 + - - +
259H ARG 3.3 4.0 - - - +
260H VAL* 4.1 2.0 - - + -
282H ILE* 3.5 16.3 - - + +
284H TRP* 3.6 18.3 - - + +
311H LEU* 3.6 31.0 - - + -
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Residues in contact with SER 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H ILE* 3.4 28.5 - - - -
233H HIS* 2.6 34.7 + - - -
237H VAL* 4.1 1.8 - - - -
239H MET 3.3 8.7 - - - -
240H VAL* 3.9 2.7 - - - -
249H ILE 4.0 0.2 + - - -
250H ALA* 1.3 74.1 - - - +
252H CYS* 1.3 60.6 + - - +
258H VAL* 3.4 6.8 - - - +
259H ARG* 2.7 27.3 + - - +
261H TRP* 3.1 12.4 + - - -
282H ILE* 3.1 10.7 - - - +
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Residues in contact with CYS 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H HIS* 4.2 0.2 + - - -
237H VAL* 3.3 3.1 - - - +
238H ARG* 2.4 34.4 + - + -
239H MET* 3.3 17.5 + - + +
251H SER* 1.3 79.0 + - - +
253H SER* 1.3 56.1 + - - +
257H THR 3.9 6.1 - - - -
258H VAL* 4.8 0.9 - - - +
279H VAL* 3.4 27.4 - - - -
280H GLU 3.6 3.4 - - - -
281H CYS 3.2 34.3 - - - -
282H ILE* 3.5 24.2 - - + -
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Residues in contact with SER 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H HIS* 2.6 25.7 - - - -
235H GLU 4.0 1.6 - - - -
236H TRP 2.6 26.2 - - - -
237H VAL* 3.8 2.5 - - - -
238H ARG* 4.1 5.8 - - - +
252H CYS* 1.3 74.4 - - - +
254H ASN* 1.3 63.0 + - - +
255H ASP* 2.4 26.2 + - - -
256H GLN 3.4 6.3 + - - -
257H THR 3.4 8.7 + - - -
278H VAL* 4.0 2.5 - - - -
279H VAL* 3.3 28.5 + - - +
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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