Contacts of the strand formed by residues 298 - 305 (chain A) in PDB entry 5WY8
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.4 7.4 - - + -
296A GLN 3.6 5.8 + - - +
297A SER* 1.3 77.2 + - - +
299A ASN* 1.3 67.8 + - - +
300A TYR* 3.5 41.9 + - + +
316A GLN* 3.5 0.3 - - - +
317A ILE* 2.9 35.2 + - + +
1103A NAG 4.5 2.9 - - - -
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Residues in contact with ASN 299 (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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271A LEU* 3.8 16.0 - - + +
272A GLY* 4.2 5.5 + - - -
297A SER* 5.3 0.2 + - - -
298A ALA* 1.3 78.8 - - - +
300A TYR* 1.3 64.8 + - - +
301A THR* 3.8 10.3 - - + +
314A ILE* 4.3 11.8 - - + +
315A ALA 3.9 4.5 - - - -
316A GLN* 3.7 19.2 - - - +
1103A NAG 1.4 74.2 + - - +
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Residues in contact with TYR 300 (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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255A ILE* 4.6 3.4 - - + -
269A TRP* 4.1 15.9 - - + -
270A MET 3.8 2.9 - - - +
271A LEU* 3.6 46.2 - - + +
276A LEU* 4.1 17.9 - - + -
289A LEU* 4.0 9.2 - - + -
291A LEU* 3.4 39.8 - - + +
294A VAL* 5.1 8.3 - - + +
298A ALA* 3.5 24.3 - - + +
299A ASN* 1.3 72.8 - - - +
301A THR* 1.3 60.0 + - - +
314A ILE* 3.2 4.2 - - - +
315A ALA* 2.8 38.9 + - + +
317A ILE* 4.2 17.5 - - + -
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Residues in contact with THR 301 (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 TRP* 3.2 7.2 - - - -
270A MET* 2.9 56.8 + - - +
272A GLY* 4.9 9.8 + - - +
299A ASN 3.8 10.8 - - - +
300A TYR* 1.3 78.4 - - - +
302A CYS* 1.3 60.9 + - - +
303A VAL* 3.9 5.5 + - - +
312A GLU* 5.0 7.4 + - - +
313A ALA 3.5 8.7 - - - -
314A ILE* 3.8 26.7 - - + -
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Residues in contact with CYS 302 (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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238A PHE* 3.5 7.7 - - + -
242A PRO* 4.4 2.7 - - + -
257A CYS* 2.0 50.5 - - + -
267A VAL* 3.5 23.1 - - - -
268A LYS 3.7 3.4 - - - -
269A TRP* 3.3 25.1 - - + -
301A THR* 1.3 72.0 - - - +
303A VAL* 1.3 60.5 + - - +
312A GLU* 3.2 3.5 - - - +
313A ALA 2.8 38.3 + - - +
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Residues in contact with VAL 303 (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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266A TYR 3.7 1.0 - - - +
267A VAL* 3.4 1.9 - - - +
268A LYS* 2.9 56.4 + - + +
270A MET* 3.6 34.5 - - + -
301A THR* 4.0 7.2 - - - +
302A CYS* 1.3 78.1 - - - +
304A ALA* 1.3 63.4 + - - +
305A MET* 4.1 7.5 + - + +
310A VAL* 3.6 28.0 - - + -
311A ILE 3.4 4.5 - - - +
312A GLU* 3.9 18.2 - - + +
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Residues in contact with ALA 304 (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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236A PRO* 4.2 2.5 - - + +
238A PHE* 4.4 6.7 - - + -
259A ALA* 3.5 32.3 - - + -
265A PRO* 4.3 6.5 - - + -
266A TYR 3.3 5.8 - - - +
267A VAL* 3.9 11.9 - - + -
302A CYS 4.1 1.0 + - - -
303A VAL* 1.3 72.3 - - - +
305A MET* 1.3 59.4 + - - +
309A GLY 4.1 1.4 - - - +
310A VAL* 3.5 1.2 - - - -
311A ILE* 2.9 49.7 + - + +
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Residues in contact with MET 305 (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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265A PRO* 3.4 2.9 - - - +
266A TYR* 2.9 41.3 + - + +
268A LYS* 4.3 24.2 - - - +
282A MET* 4.8 9.9 - - - +
303A VAL* 4.0 5.6 - - + -
304A ALA* 1.3 74.6 - - - +
306A SER* 1.3 60.9 + - - +
309A GLY 3.4 4.7 - - - +
310A VAL* 3.9 25.4 - - + +
73B SER* 3.8 33.7 - - - +
75B MET* 3.7 18.8 - - - +
77B TYR* 4.4 0.2 + - - -
121B ARG* 4.4 21.8 - - + +
122B ASN* 5.4 3.1 - - - -
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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