Contacts of the strand formed by residues 314 - 321 (chain D) in PDB entry 5VZU
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 LEU 314 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D PRO* 4.2 23.8 - - + +
177D PRO* 3.6 41.7 - - + +
178D HIS 4.0 6.3 - - - +
179D ASP* 3.5 27.3 + - - +
180D PRO* 4.0 7.0 - - + +
182D VAL* 3.9 21.3 - - + +
273D LYS* 5.9 1.4 + - - -
306D LYS* 4.8 2.5 - - + -
307D GLY 3.3 8.7 - - - +
308D THR* 3.6 30.5 - - + -
312D HIS 4.3 2.9 - - - +
313D GLY* 1.3 74.6 - - - -
315D GLU* 1.3 66.1 + - - +
332D THR* 4.6 1.4 + - - -
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D PRO* 5.5 1.3 - - - -
306D LYS* 4.8 0.4 - - - -
307D GLY* 2.8 32.3 + - - +
309D TYR* 3.5 25.4 - - + +
312D HIS* 3.4 15.5 - - + +
313D GLY 4.1 1.3 - - - +
314D LEU* 1.3 81.2 - - - +
316D ILE* 1.3 65.7 + - - +
317D VAL* 3.8 4.7 + - + +
330D LYS* 2.7 32.5 + - - +
332D THR* 3.5 16.4 - - - +
333D GLY* 3.4 18.9 - - - +
334D ASP* 2.5 30.2 - - - +
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 4.6 15.5 - - + -
174D TYR 4.6 2.7 - - - +
176D PRO* 4.0 20.4 - - + -
186D MET* 3.4 33.9 - - + -
304D LEU* 4.3 20.6 - - + -
305D PHE 3.3 10.5 - - - +
306D LYS* 5.1 3.4 - - + -
315D GLU* 1.3 73.6 - - - +
317D VAL* 1.3 63.2 + - - +
331D ILE* 2.8 45.2 + - + -
332D THR* 3.1 36.1 + - + +
512D VAL* 5.2 2.7 - - + -
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D LEU* 3.6 1.4 - - - -
305D PHE* 2.7 44.0 + - + +
309D TYR* 3.5 35.9 - - + +
315D GLU* 4.2 5.6 - - + +
316D ILE* 1.3 80.1 - - - +
318D MET* 1.3 63.7 + - - +
319D LEU* 3.9 1.0 + - + +
328D GLY* 4.0 13.2 - - - -
329D THR 3.5 20.4 - - - +
330D LYS* 4.6 9.0 - - + -
331D ILE* 4.6 2.5 - - - -
343D THR* 4.1 10.8 - - + -
344D VAL* 5.9 1.3 - - + -
496D PHE* 5.5 5.8 - - + -
509D TYR* 4.2 19.1 - - + -
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Residues in contact with MET 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D ILE* 5.8 2.7 - - + -
290D TYR 3.5 26.7 - - - +
291D LEU* 4.5 1.1 - - - -
292D PRO* 3.8 24.2 - - + -
303D GLY 3.6 3.8 - - - +
304D LEU* 3.6 27.8 - - + -
317D VAL* 1.3 72.8 - - - +
319D LEU* 1.3 62.9 + - - +
320D SER* 3.7 1.5 + - - +
327D ARG 3.2 5.4 - - - +
328D GLY* 3.4 0.2 - - - -
329D THR* 2.7 46.2 + - + +
331D ILE* 4.0 19.5 - - + +
527D PHE* 3.6 22.0 - - + -
530D MET* 4.1 5.4 - - + -
531D LEU* 3.9 17.0 - - + -
534D ILE* 5.9 0.7 - - + -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D PRO* 3.4 5.4 - - - +
300D ILE 5.6 1.8 - - - +
301D LYS 4.7 4.7 - - - +
302D PRO* 3.3 7.1 - - + +
303D GLY 3.0 24.6 + - - +
305D PHE* 3.6 28.0 - - + -
317D VAL* 3.9 2.4 + - + +
318D MET* 1.3 71.8 - - - +
320D SER* 1.3 64.6 + - - +
321D PHE* 4.3 22.0 - - + -
326D ALA* 4.0 25.4 - - + -
327D ARG 3.3 12.3 - - - +
328D GLY* 4.6 3.4 - - - +
344D VAL* 5.9 1.8 - - + -
346D ILE* 5.6 3.1 - - + -
488D PHE* 5.6 7.9 - - + -
496D PHE* 3.9 31.6 - - + -
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Residues in contact with SER 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D PRO* 3.7 8.3 - - - -
318D MET* 4.9 3.1 - - - -
319D LEU* 1.3 76.4 - - - +
321D PHE* 1.3 67.4 + - - +
322D HIS* 2.9 22.6 + - - -
326D ALA* 3.6 2.3 - - - +
327D ARG* 2.7 48.0 + - - +
329D THR* 5.1 1.1 + - - -
527D PHE* 3.4 34.5 - - - -
531D LEU* 4.2 3.8 - - - +
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Residues in contact with PHE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D PRO* 5.3 0.8 - - - +
293D PRO* 5.3 9.8 + - - +
295D ARG* 6.4 0.2 - - - -
298D ASP 4.0 11.9 - - - +
299D LEU* 3.3 33.0 - - + -
300D ILE* 3.5 28.5 - - + -
301D LYS 3.4 31.0 - - - -
302D PRO* 3.6 26.4 - - + +
319D LEU* 4.3 18.8 - - + -
320D SER* 1.3 74.3 - - - +
322D HIS* 1.3 70.5 + - - +
323D GLY 4.0 3.8 - - - +
325D ARG 3.8 1.3 - - - -
326D ALA* 4.2 23.6 - - + -
348D LEU* 4.3 15.3 - - + -
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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