Contacts of the strand formed by residues 310 - 319 (chain B) in PDB entry 5YL4
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 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B MET* 5.0 2.5 - - - -
294B PHE* 4.5 11.2 + + - -
299B MET* 3.7 9.0 - - - +
305B PRO* 3.2 37.2 - - + +
309B ARG* 1.3 70.5 - - - +
311B LEU* 1.3 62.7 + - - +
312B THR 4.2 5.6 - - - +
313B VAL* 3.8 18.6 - - + -
340B TYR* 2.7 27.1 + - + +
341B PHE* 3.9 28.0 - + + -
342B VAL* 3.1 26.7 + - - +
348B ASN* 3.4 3.1 + - - -
367B PHE* 3.4 33.4 - + - -
369B GLY* 4.2 6.5 - - - -
370B ASN 3.9 1.3 - - - -
371B SER* 3.8 24.9 - - - -
505B MES 4.1 17.7 - - - -
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Residues in contact with LEU 311 (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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259B PRO* 4.0 28.7 - - + -
260B PHE* 4.7 1.6 - - + -
263B LEU* 4.4 25.1 - - + -
310B TYR* 1.3 73.2 - - - +
312B THR* 1.3 69.5 + - - +
342B VAL* 4.0 14.5 - - + +
344B TRP* 4.0 27.1 - - + -
345B ILE* 3.5 10.9 - - + +
348B ASN* 3.1 19.3 + - - +
370B ASN* 2.8 35.6 + - - +
372B THR* 3.9 27.8 - - + +
422B TYR* 5.2 1.6 - - + -
425B TYR* 4.5 4.3 - - + -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 5.1 2.0 - - + -
404A PHE* 4.1 17.5 - - + -
256B ASN 3.6 18.8 - - - +
257B MET* 3.0 47.0 + - - +
259B PRO* 4.6 2.7 - - + -
310B TYR* 4.2 1.2 - - - -
311B LEU* 1.3 82.9 - - - +
313B VAL* 1.3 68.9 + - - +
345B ILE* 4.7 2.2 - - + -
348B ASN* 3.5 17.7 - - + +
370B ASN* 3.1 31.2 + - - +
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Residues in contact with VAL 313 (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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257B MET* 4.3 6.4 - - - +
294B PHE* 4.1 10.3 - - + -
310B TYR* 3.8 22.0 - - + -
312B THR* 1.3 79.7 - - - +
314B ALA* 1.3 73.8 + - - +
315B ALA* 5.2 1.3 - - + -
341B PHE* 3.7 28.5 - - + -
348B ASN* 3.0 9.8 + - - +
349B VAL* 4.0 15.9 - - + -
350B LYS* 3.1 24.8 + - - +
367B PHE* 3.4 30.3 - - + -
368B ILE 3.5 6.7 - - - +
506B 8WR 5.2 0.5 - - - -
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B MET* 3.9 7.4 - - + +
313B VAL* 1.3 78.1 - - - +
315B ALA* 1.3 62.9 + - - +
350B LYS 3.3 6.7 - - - -
367B PHE* 3.8 0.5 - - - -
368B ILE* 2.9 43.4 + - + +
506B 8WR 3.2 50.0 - - + +
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Residues in contact with ALA 315 (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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293B MET* 3.7 21.5 - - + -
313B VAL* 5.2 3.1 - - + -
314B ALA* 1.3 76.8 - - - +
316B ILE* 1.3 62.6 + - - +
317B PHE* 4.0 10.3 - - + -
330B MET* 4.1 25.8 - - + -
350B LYS 3.1 7.7 + - - +
351B THR* 3.3 5.4 - - - +
352B ALA 3.1 22.3 + - - -
366B THR 3.4 6.5 - - - -
367B PHE* 5.0 2.0 - - + -
506B 8WR 3.3 3.2 - - - +
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Residues in contact with ILE 316 (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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235B GLY 3.4 21.3 - - - +
238B THR* 3.4 34.1 - - + -
239B CYS* 4.8 7.6 - - + +
293B MET* 4.7 0.2 - - - +
315B ALA* 1.3 79.3 - - - +
317B PHE* 1.3 65.1 + - - +
318B ARG* 3.9 15.7 + - + +
352B ALA* 3.6 11.4 - - + +
353B VAL 5.4 0.2 - - - -
354B CYS* 4.4 4.9 - - + +
365B ALA* 3.6 1.2 - - - -
366B THR* 3.0 34.5 + - - +
368B ILE* 4.9 5.8 - - + -
506B 8WR 3.6 43.1 - - + +
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Residues in contact with PHE 317 (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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286B VAL* 4.7 3.8 - - + -
289B LEU* 3.9 23.1 - - + -
290B THR* 3.7 24.0 - - - -
293B MET* 4.0 9.2 - - - -
315B ALA* 4.2 9.2 - - + -
316B ILE* 1.3 75.2 - - - +
318B ARG* 1.3 61.7 + - - +
321B MET* 3.8 22.9 - - + -
326B VAL* 3.6 29.4 - - + -
330B MET* 3.8 19.5 - - - -
351B THR* 3.6 25.4 - - + -
352B ALA 2.9 10.6 + - - +
353B VAL* 3.3 7.3 - - + +
354B CYS* 2.8 26.2 + - - +
364B SER 3.5 2.9 - - - -
365B ALA* 3.8 21.3 - - + -
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Residues in contact with ARG 318 (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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27B GLU* 3.0 35.9 + - - -
234B SER* 3.2 17.2 + - - -
235B GLY* 5.0 5.8 - - - +
238B THR* 3.1 33.6 + - + +
242B PHE* 3.6 16.3 - - - -
270B PHE* 6.2 1.6 - - - -
316B ILE* 3.9 17.5 - - + +
317B PHE* 1.3 76.8 - - - +
319B GLY* 1.3 58.1 + - - +
321B MET* 3.2 11.7 - - - +
354B CYS* 3.3 4.7 - - + -
356B ILE* 3.1 27.3 + - - +
357B PRO* 3.8 10.1 + - - -
358B PRO* 3.9 23.6 - - + +
363B MET* 3.2 5.1 - - - -
364B SER* 2.8 46.4 + - - +
366B THR* 5.6 2.0 - - - +
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Residues in contact with GLY 319 (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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318B ARG* 1.3 74.2 - - - +
320B ARG* 1.3 60.7 + - - -
321B MET* 3.3 18.3 + - - +
353B VAL* 4.1 5.5 - - - +
354B CYS 2.8 17.1 + - - +
355B ASP* 3.6 21.8 + - - +
356B ILE 4.3 1.4 + - - -
357B PRO* 4.2 7.6 - - - -
362B LYS 3.8 14.4 - - - -
363B MET* 4.3 0.9 - - - -
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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