Contacts of the strand formed by residues 330 - 336 (chain A) in PDB entry 1YHV
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 TYR 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ILE* 4.5 4.7 + - - +
316A ILE* 3.4 42.3 - - + +
319A MET* 3.8 35.7 - - + -
320A ARG* 4.1 38.8 - - + -
323A LYS* 3.0 35.8 + - - +
328A VAL 3.4 3.6 + - - -
329A ASN* 1.3 74.6 + - - +
331A LEU* 1.3 63.0 + - - +
332A ASP* 3.4 33.2 + - - -
333A SER* 2.8 25.1 + - - -
342A VAL* 4.1 4.3 - - + -
343A VAL 4.0 5.4 - - - -
344A MET* 3.7 7.9 - - - -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 5.6 0.3 + - - -
270A TYR* 5.6 1.3 - - + +
289A ASP* 5.7 2.7 - - - +
294A GLN* 4.0 20.9 - - - +
296A VAL* 3.6 30.3 - - + -
329A ASN* 3.1 39.3 - - + +
330A TYR* 1.3 80.1 - - - +
332A ASP* 1.3 65.7 + - + +
343A VAL* 2.8 22.7 + - + +
344A MET 3.8 2.0 - - - -
345A GLU* 3.7 19.5 - - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A SER* 2.5 28.5 + - - -
269A LYS* 3.2 15.1 + - - +
270A TYR* 4.3 10.3 - - - +
330A TYR* 3.4 19.0 + - - -
331A LEU* 1.3 84.3 - - + +
333A SER* 1.3 72.7 + - - +
334A TYR* 3.0 31.9 + - + -
343A VAL* 2.8 28.5 + - + +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ILE* 4.1 7.1 + - - +
261A VAL* 3.6 24.5 - - - +
262A SER* 2.9 25.3 + - - -
316A ILE* 4.7 4.5 - - - -
330A TYR* 2.8 24.1 + - - -
332A ASP* 1.3 83.2 + - - +
334A TYR* 1.3 71.9 + - - +
340A LEU* 4.7 2.9 - - - -
341A TRP 3.1 13.5 - - - -
342A VAL* 4.5 8.3 - - - -
343A VAL 4.7 0.2 - - - +
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Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL* 3.8 7.4 - - - -
262A SER* 3.6 28.6 - - - -
263A VAL 3.7 11.7 - - - -
264A GLY 3.7 16.8 - - - +
265A ASP 4.7 2.2 - - - -
266A PRO* 3.4 48.9 - - + -
269A LYS* 3.4 22.6 + - + +
270A TYR* 4.0 14.4 - + - -
332A ASP* 3.0 33.7 + - + -
333A SER* 1.3 76.8 - - - +
335A LEU* 1.3 62.7 + - - +
336A VAL* 4.2 0.7 - - + -
339A GLU 3.9 0.3 - - - +
340A LEU* 3.3 5.9 - - - +
341A TRP* 2.9 34.9 + - + -
343A VAL* 4.4 8.1 - - + -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 4.1 18.2 - - + +
257A LEU* 4.2 12.6 - - + -
258A ARG* 4.1 27.6 - - + +
261A VAL* 4.0 21.8 - - + +
262A SER 4.6 1.4 + - - -
264A GLY 4.1 7.5 + - - +
303A LEU* 3.5 28.3 - - + -
334A TYR* 1.3 76.4 - - - +
336A VAL* 1.3 63.0 - - - +
337A GLY 3.5 18.1 + - - +
339A GLU 3.4 16.8 - - - +
340A LEU* 3.9 12.3 - - + -
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLY 3.9 15.5 - - - +
265A ASP* 3.7 26.7 - - + +
266A PRO* 4.1 13.0 - - + -
334A TYR* 5.1 0.4 - - + -
335A LEU* 1.3 78.4 - - - +
337A GLY* 1.3 60.8 + - - +
338A ASP 3.4 0.2 + - - -
339A GLU* 2.7 43.5 + - + +
341A TRP* 4.8 7.4 - - + +
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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