Contacts of the strand formed by residues 283 - 288 (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 THR 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A LYS* 3.4 37.8 + - + +
277A GLY 3.5 5.6 - - - +
278A GLN* 4.1 4.4 - - - +
282A GLY* 1.3 72.6 - - - -
284A VAL* 1.3 62.8 + - - +
285A TYR* 3.2 40.1 + - + +
298A ILE 3.5 2.1 - - - +
299A ARG* 3.4 0.7 - - - -
300A GLN* 2.8 41.1 + - - -
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 3.6 2.1 - - - +
276A ILE* 2.6 38.5 + - + -
277A GLY* 2.9 26.0 + - - +
281A SER* 6.0 3.8 - - - -
282A GLY 4.3 8.1 - - - +
283A THR* 1.3 77.0 - - - +
285A TYR* 1.3 65.0 + - - +
297A ALA* 4.8 11.0 - - + -
298A ILE 3.3 12.3 - - - +
299A ARG* 4.3 18.4 - - + +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 6.2 1.3 - - - -
273A PHE* 3.8 34.1 - + + -
274A GLU 3.0 8.5 - - - +
275A LYS* 3.6 32.9 + - + +
276A ILE* 4.3 1.3 - - - +
283A THR* 3.2 38.0 + - + +
284A VAL* 1.3 79.7 - - - +
286A THR* 1.3 62.7 + - - +
297A ALA* 3.3 4.4 - - - -
298A ILE* 2.7 46.8 + - + +
300A GLN* 3.3 38.6 + - + -
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Residues in contact with THR 286 (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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272A ARG 3.5 3.2 - - - +
273A PHE* 3.2 4.7 - - - -
274A GLU* 2.7 45.6 + - + -
276A ILE* 3.9 18.4 - - - +
285A TYR* 1.3 73.2 - - - +
287A ALA* 1.3 65.3 + - - +
295A GLU* 2.8 38.6 - - + +
296A VAL 3.3 5.8 - - - +
297A ALA* 4.6 0.9 - - - +
346A TYR* 3.9 23.6 - - + -
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Residues in contact with ALA 287 (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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270A TYR* 4.1 5.6 - - + -
271A THR 4.8 0.2 - - - +
272A ARG* 3.9 8.7 - - - -
273A PHE* 4.1 25.4 - - + +
285A TYR 4.1 0.2 + - - -
286A THR* 1.3 79.1 - - - +
288A MET* 1.3 59.8 + - - +
295A GLU* 3.3 8.8 - - - +
296A VAL* 2.6 39.7 + - + -
298A ILE* 4.0 27.1 - - + -
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Residues in contact with MET 288 (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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270A TYR* 3.1 7.4 - - - -
271A THR* 2.9 31.8 + - - +
272A ARG* 4.5 17.5 - - + +
287A ALA* 1.3 76.6 - - - +
289A ASP* 1.3 68.8 + - - +
290A VAL* 3.2 7.6 + - + +
293A GLY* 3.2 31.4 - - - +
294A GLN 3.6 2.5 - - - +
295A GLU* 4.8 6.5 - - + -
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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