Contacts of the strand formed by residues 294 - 298 (chain B) in PDB entry 4YVF
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 ALA 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLY 4.3 5.4 - - - +
270B ASN* 3.4 13.7 - - - +
272B PHE* 4.1 10.8 - - + -
290B MET* 3.9 30.1 - - + -
291B LYS* 3.2 19.0 + - + +
292B ASP 3.2 1.3 - - - -
293B ASP* 1.3 75.7 - - - +
295B ILE* 1.3 61.0 + - - +
296B VAL 3.8 0.7 + - - -
335B ARG 3.5 2.2 + - - -
336B ILE* 3.7 7.1 - - + +
337B ILE 2.8 24.9 + - - +
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.4 11.9 - - + -
207B THR* 3.7 28.7 - - + +
209B VAL* 3.7 25.1 - - + -
214B LYS* 5.6 2.0 - - - -
270B ASN 2.9 13.4 + - - +
271B ILE* 3.2 17.4 - - + -
272B PHE* 2.6 33.8 + - - +
293B ASP 3.9 8.7 - - - +
294B ALA* 1.3 73.7 - - - +
296B VAL* 1.3 59.4 + - - +
297B CYS* 5.2 1.1 - - + +
337B ILE* 3.4 19.5 - - + +
339B LEU* 3.8 33.9 - - + -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.6 5.4 - - + -
282B ILE* 3.8 19.5 - - + -
287B PHE* 4.3 6.1 - - + -
290B MET* 3.8 27.1 - - + -
294B ALA 4.1 2.2 - - - +
295B ILE* 1.3 77.9 - - - +
297B CYS* 1.3 65.0 + - - +
306B ILE* 3.6 31.2 - - + -
336B ILE* 3.7 24.0 - - + -
337B ILE 2.8 11.7 + - - +
338B LEU* 3.6 11.3 - - + +
339B LEU* 3.1 25.5 + - - +
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Residues in contact with CYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B LEU* 4.3 4.9 - - - -
203B ILE* 4.3 12.1 - - - -
271B ILE* 5.3 1.6 - - - -
272B PHE 2.8 22.2 + - - +
273B VAL* 3.2 23.3 - - - -
274B THR* 3.0 23.2 + - - +
295B ILE* 5.4 0.9 - - - -
296B VAL* 1.3 79.3 - - - +
298B ASN* 1.3 61.2 + - - +
306B ILE* 3.5 8.2 - - - +
339B LEU* 4.0 26.2 - - + +
345B VAL* 4.0 24.9 - - + -
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 2.5 34.1 + - - +
297B CYS* 1.3 75.2 - - - +
299B ILE* 1.3 60.8 + - - +
300B GLY 3.1 8.3 + - - +
301B HIS 3.1 28.5 + - - +
302B PHE 3.3 16.0 + - - -
303B ASP* 4.1 1.6 - - - +
305B GLU* 3.3 17.0 - - - +
306B ILE* 3.6 9.6 - - + +
339B LEU 5.2 0.4 + - - -
342B GLY 3.3 19.7 + - - +
343B ARG 2.8 22.2 + - - +
344B LEU* 3.2 2.8 - - - +
345B VAL* 2.8 14.8 + - - -
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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