Contacts of the strand formed by residues 253 - 262 (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 VAL 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A HIS* 3.7 37.7 - - + -
247A ILE* 4.6 13.7 - - + -
252A SER* 1.3 75.1 - - - +
254A ASN* 1.3 75.8 + - - +
255A ILE* 4.0 14.1 - - + -
289A LEU 3.9 0.3 - - - +
290A GLU* 3.8 0.2 - - - -
291A LEU* 2.9 62.1 + - + +
294A VAL* 5.6 2.9 - - + +
317A ILE* 4.7 9.4 - - + -
1C NAG 4.2 2.9 - - - -
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Residues in contact with ASN 254 (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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253A VAL* 1.3 88.6 - - - +
255A ILE* 1.3 62.7 + - - +
256A THR* 4.1 7.3 + - + +
288A VAL* 4.2 16.1 - - + +
289A LEU 3.5 3.8 - - - -
290A GLU* 3.3 21.2 - - - +
291A LEU 5.1 0.2 - - - +
1C NAG 1.4 74.5 + - + +
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Residues in contact with ILE 255 (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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242A PRO* 4.1 15.7 - - + -
243A THR* 4.2 19.7 - - + +
245A HIS* 5.9 1.3 - - + -
253A VAL* 4.0 14.8 - - + -
254A ASN* 1.3 76.2 - - - +
256A THR* 1.3 66.3 + - - +
269A TRP* 4.0 25.7 - - + -
287A ASN 4.0 0.9 - - - +
288A VAL* 3.3 3.2 - - - -
289A LEU* 2.9 41.6 + - + +
291A LEU* 4.0 15.7 - - + -
300A TYR* 4.6 7.9 - - + -
315A ALA* 4.3 8.1 - - + -
317A ILE* 3.8 33.9 - - + -
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Residues in contact with THR 256 (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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240A ILE* 3.8 23.2 - - - +
241A PRO 4.0 2.3 - - - +
242A PRO* 3.7 18.4 - - - +
243A THR* 4.8 5.6 + - - +
254A ASN* 4.1 7.6 + - + +
255A ILE* 1.3 77.3 - - - +
257A CYS* 1.3 60.8 + - - +
258A VAL* 4.3 6.5 - - - -
269A TRP* 4.6 1.1 - - - -
286A ARG* 5.1 9.4 - - - +
287A ASN 3.9 3.4 - - - -
288A VAL* 3.8 24.0 - - + -
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Residues in contact with CYS 257 (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* 3.4 22.7 - - - -
240A ILE 3.5 3.4 - - - -
242A PRO* 4.4 7.2 - - + -
255A ILE 4.1 0.2 + - - -
256A THR* 1.3 73.8 - - - +
258A VAL* 1.3 64.7 + - - +
259A ALA 5.0 0.2 - - - -
267A VAL* 4.1 4.0 - - + +
269A TRP* 3.6 13.9 - - + -
285A GLY 4.0 0.9 - - - +
286A ARG* 3.5 1.7 - - - -
287A ASN 2.9 36.3 + - - +
302A CYS* 2.0 53.2 - - + -
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Residues in contact with VAL 258 (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* 3.7 4.3 - - - -
239A SER* 2.8 43.6 + - - +
240A ILE* 2.9 46.4 + - + +
256A THR* 5.2 3.4 - - - -
257A CYS* 1.3 80.0 - - - +
259A ALA* 1.3 56.9 + - - +
260A VAL* 4.5 7.0 - - + -
285A GLY 3.3 9.2 - - - +
286A ARG* 3.7 35.4 - - + +
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Residues in contact with ALA 259 (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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237A ARG 3.3 19.3 - - - +
238A PHE* 4.1 9.0 - - + -
239A SER 3.9 0.7 - - - +
257A CYS* 4.2 0.6 - - - -
258A VAL* 1.3 75.1 - - - +
260A VAL* 1.3 67.0 + - - +
264A MET* 4.3 0.3 - - - +
265A PRO* 3.7 11.9 - - + +
267A VAL* 4.2 4.0 - - + +
285A GLY* 2.7 33.0 + - - +
304A ALA* 3.5 32.3 - - + -
311A ILE* 4.8 0.9 - - + -
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Residues in contact with VAL 260 (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* 3.4 5.0 - - - +
237A ARG* 3.0 67.8 + - - +
239A SER* 3.9 21.1 - - - +
258A VAL* 4.5 8.3 - - + -
259A ALA* 1.3 79.4 - - - +
261A GLY* 1.3 60.7 + - - +
264A MET* 3.8 23.6 - - + -
265A PRO* 3.7 5.6 - - - -
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Residues in contact with GLY 261 (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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234A VAL* 4.0 17.5 - - - -
235A PRO 4.4 3.6 - - - -
236A PRO* 4.6 1.8 - - - -
237A ARG* 6.1 0.4 - - - -
260A VAL* 1.3 80.2 - - - +
262A SER* 1.3 60.6 + - - -
263A PRO 3.2 19.0 - - - -
264A MET* 3.2 16.2 + - - +
265A PRO* 3.9 1.3 - - - +
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Residues in contact with SER 262 (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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232A ARG 3.3 19.7 + - - -
233A ARG* 3.3 4.5 - - - -
234A VAL* 3.0 44.9 + - - +
261A GLY* 1.3 75.2 - - - -
263A PRO* 1.3 60.9 + - - +
308A LEU* 3.3 5.5 - - - +
85B PHE* 3.2 23.1 - - - -
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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