Contacts of the strand formed by residues 422 - 428 (chain D) in PDB entry 6B5G
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 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D VAL* 3.3 13.0 - - - +
313D PHE* 4.0 0.4 - - - -
324D SER* 5.3 5.0 - - - -
371D ILE* 3.9 16.6 - - + -
375D ILE* 3.8 31.2 - - + -
402D THR* 3.3 8.3 - - + +
404D PHE* 3.8 33.2 - - + -
418D ILE* 3.9 29.9 - - + +
420D GLY 2.6 13.3 + - - +
421D PRO* 1.3 79.5 - - + +
423D GLN* 1.3 62.0 + - - +
424D GLU* 4.0 11.0 + - + +
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Residues in contact with GLN 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D VAL 5.3 0.4 + - - -
308D ALA* 3.3 18.6 + - - +
309D HIS* 3.7 16.0 + - - +
312D VAL* 3.7 9.2 - - + +
313D PHE* 3.8 18.1 - - + -
326D ILE* 3.2 32.3 - - + +
340D SER* 3.5 31.0 + - - +
402D THR 2.7 15.6 + - - +
403D VAL* 3.5 15.7 - - + +
404D PHE* 2.7 35.0 + - - +
422D VAL* 1.3 74.3 - - - +
424D GLU* 1.3 60.0 + - - +
425D ILE* 4.2 10.5 - - + -
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Residues in contact with GLU 424 (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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290D LYS* 2.7 26.5 + - - -
312D VAL* 5.4 0.4 - - - +
324D SER* 3.3 22.5 + - - +
326D ILE* 3.1 29.7 + - - +
404D PHE* 3.9 4.5 - - + -
407D VAL* 3.9 15.8 - - + +
413D ILE* 2.7 44.0 - - + +
414D ALA* 3.4 5.6 + - - -
418D ILE* 3.2 16.8 - - - +
422D VAL* 4.1 13.0 - - + +
423D GLN* 1.3 80.9 - - - +
425D ILE* 1.3 61.2 + - - +
426D LEU* 3.8 4.1 - - + +
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Residues in contact with ILE 425 (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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326D ILE* 3.4 5.4 - - + +
328D VAL* 3.8 24.9 - - + -
333D TYR* 3.5 18.8 + - + -
336D PHE* 4.0 9.9 - - + -
337D VAL* 4.0 22.0 - - + -
340D SER* 3.9 25.4 - - - +
403D VAL* 3.9 24.0 - - + -
404D PHE 3.2 9.2 + - - +
405D SER 2.5 31.1 - - - +
407D VAL* 3.3 11.2 + - - +
423D GLN* 4.2 13.9 - - + +
424D GLU* 1.3 77.3 - - - +
426D LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 426 (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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325D ARG* 3.9 25.1 - - + -
326D ILE 2.7 15.2 + - - +
327D PHE* 3.6 21.3 - - + -
328D VAL* 2.9 24.5 + - - +
333D TYR* 3.5 11.8 - - - -
407D VAL* 3.2 42.6 - - + +
408D THR 4.2 1.3 - - - -
409D ASP* 3.1 33.0 - - - +
414D ALA* 4.9 4.3 - - + -
424D GLU* 3.8 12.8 - - + +
425D ILE* 1.3 76.7 - - - +
427D ARG* 1.3 62.1 + - - +
437D ARG* 3.6 7.0 - - - +
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Residues in contact with ARG 427 (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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327D PHE* 5.2 0.4 - - - -
328D VAL 3.4 6.5 - - - +
330D GLU* 3.0 40.7 + - - +
333D TYR* 3.6 29.2 - - + -
334D GLU* 3.5 19.8 + - - -
406D ASN* 3.1 38.2 - - - +
407D VAL 4.7 3.7 + - - +
426D LEU* 1.3 74.9 - - - +
428D PHE* 1.3 55.6 + - - +
437D ARG* 2.7 31.8 + - - +
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Residues in contact with PHE 428 (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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294D ILE* 3.9 17.7 - - + -
295D ILE 3.5 15.7 - - - -
296D PHE* 4.0 23.6 - + - -
327D PHE* 3.7 16.2 - - + -
328D VAL 3.1 34.2 + - - -
329D GLU* 3.1 37.0 - - + -
330D GLU* 2.9 28.0 + - - +
427D ARG* 1.3 77.0 - - - +
429D LYS* 1.3 65.3 + - - +
430D THR 3.6 15.5 - - - -
433D GLU* 3.7 11.2 - - - +
434D VAL* 3.6 27.4 - - + -
437D ARG* 3.6 11.9 - - - +
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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