Contacts of the strand formed by residues 392 - 403 (chain B) in PDB entry 6ZGI
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 PHE 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ALA* 4.6 11.4 - - + -
387B LEU* 3.6 46.2 - - + -
390B LEU* 3.7 25.1 - - + -
391B CYS* 1.3 74.1 - - - +
393B THR* 1.3 62.5 + - - +
394B ASN 4.3 0.3 + - - -
395B VAL* 3.6 21.0 - - + +
515B PHE* 3.9 25.8 - + + -
516B GLU 3.8 2.5 - - - -
517B LEU* 3.6 24.0 - - + -
522B ALA* 3.5 10.7 - - - +
523B THR* 3.7 10.2 + - - +
524B VAL* 3.7 29.2 + - + +
525B CYS 4.0 5.1 - - - +
526B GLY* 4.3 7.9 - - - -
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Residues in contact with THR 393 (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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391B CYS 5.0 0.9 + - - -
392B PHE* 1.3 73.4 - - - +
394B ASN* 1.3 89.5 + - - +
395B VAL 3.5 0.9 - - - -
515B PHE* 3.5 2.1 - - - -
516B GLU* 2.9 51.0 + - - +
517B LEU 6.0 0.2 - - - -
518B LEU 5.1 4.5 + - - -
519B HIS 5.3 0.2 + - - -
520B ALA* 3.5 35.0 + - + -
521B PRO 3.7 15.0 - - - +
522B ALA* 3.6 13.5 - - - +
523B THR 5.4 0.2 - - - +
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Residues in contact with ASN 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 3.1 39.7 - - - +
392B PHE 4.3 0.6 + - - -
393B THR* 1.3 91.9 - - - +
395B VAL* 1.3 62.3 + - - +
396B TYR* 3.6 12.3 + - + -
514B SER* 3.2 11.3 + - - +
515B PHE* 3.8 2.8 - - - -
516B GLU* 3.3 19.1 - - - +
520B ALA* 5.7 0.2 - - - +
523B THR* 6.1 2.4 - - - +
200C TYR* 5.4 2.3 + - + +
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 3.8 5.6 - - - +
358B ILE* 3.0 63.3 + - + +
392B PHE* 3.6 35.0 - - + +
394B ASN* 1.3 74.4 - - - +
396B TYR* 1.3 69.3 + - - +
513B LEU* 5.3 7.0 - - + -
514B SER 3.3 7.6 - - - +
515B PHE* 3.8 16.8 - - + -
524B VAL* 3.8 18.2 - - + -
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Residues in contact with TYR 396 (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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355B ARG* 3.9 30.7 - - + +
356B LYS 3.4 16.6 - - - -
357B ARG* 3.5 53.4 + - + -
358B ILE* 4.7 0.9 - - - +
394B ASN* 3.8 15.5 - - + -
395B VAL* 1.3 75.7 - - - +
397B ALA* 1.3 59.7 + - - +
398B ASP* 4.7 2.0 - - - +
512B VAL 3.6 1.3 - - - +
513B LEU* 3.4 6.2 - - - +
514B SER* 2.9 38.9 + - - +
200C TYR* 4.0 30.6 - + - -
228C ASP 4.9 2.8 + - - -
230C PRO* 3.4 33.0 - - + +
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.4 19.3 - - + -
354B ASN* 3.7 1.6 + - - +
355B ARG* 3.5 1.9 - - - -
356B LYS* 2.9 42.4 + - + +
358B ILE* 3.9 15.5 - - + +
396B TYR* 1.3 73.4 - - - +
398B ASP* 1.3 63.4 + - - +
399B SER* 4.8 3.1 + - - +
511B VAL* 4.4 3.1 - - + -
512B VAL 3.4 4.9 - - - +
513B LEU* 3.8 20.2 - - + -
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Residues in contact with ASP 398 (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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353B TRP* 4.0 12.1 - - + -
354B ASN 3.0 7.9 - - - +
355B ARG* 3.3 43.0 + - - +
396B TYR* 4.7 1.6 - - - +
397B ALA* 1.3 77.1 + - - +
399B SER* 1.3 63.4 + - - +
400B PHE* 4.8 4.2 - - + -
423B TYR* 2.7 30.0 + - + +
464B PHE* 3.9 6.2 - - - -
510B VAL 3.6 0.7 - - - +
511B VAL* 3.1 7.4 - - - +
512B VAL* 2.9 44.9 + - + +
514B SER* 5.4 4.1 - - - -
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.7 8.3 + - - +
347B PHE* 3.8 22.2 - - - -
348B ALA* 4.0 5.6 - - - +
353B TRP* 3.9 0.7 - - - -
354B ASN* 2.9 44.3 + - - +
397B ALA* 4.8 3.6 + - - +
398B ASP* 1.3 77.3 + - - +
400B PHE* 1.3 68.3 + - - +
510B VAL 3.4 3.8 - - - -
511B VAL* 3.9 14.6 - - - +
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Residues in contact with PHE 400 (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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347B PHE* 3.5 10.2 - - - -
348B ALA 3.6 11.0 - - - +
349B SER 4.2 2.7 - - - +
350B VAL* 3.7 36.8 - - + -
353B TRP* 3.9 14.6 - - + -
398B ASP* 4.9 4.0 - - + -
399B SER* 1.3 82.4 - - - +
401B VAL* 1.3 65.3 + - - +
402B ILE* 3.9 17.3 - - + -
410B ILE* 4.1 23.6 - - + -
423B TYR* 4.1 35.9 - + - -
510B VAL* 2.9 62.6 + - + +
512B VAL* 4.6 6.1 - - + -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 3.5 27.8 - - + -
348B ALA 3.4 4.7 + - - +
350B VAL* 3.9 13.7 + - - +
400B PHE* 1.3 75.3 - - - +
402B ILE* 1.3 75.5 + - - +
442B ASP* 4.6 2.9 - - - +
451B TYR* 3.8 38.1 - - + +
495B TYR* 4.5 7.4 - - - -
497B PHE* 4.3 16.2 - - + -
507B PRO* 4.4 9.9 - - + -
508B TYR 3.3 9.4 - - - +
509B ARG* 3.7 22.0 - - + +
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Residues in contact with ILE 402 (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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350B VAL* 3.8 27.4 - - + -
400B PHE* 3.9 7.0 - - + -
401B VAL* 1.3 80.1 - - - +
403B ARG* 1.3 65.9 + - - +
406B GLU* 3.8 20.6 - - + +
407B VAL* 3.9 32.1 - - + -
410B ILE* 4.1 14.1 - - + -
418B ILE* 4.6 8.1 - - + -
495B TYR* 4.3 8.3 - - - +
497B PHE* 4.4 5.6 - - - -
507B PRO* 3.6 4.7 - - - +
508B TYR* 2.9 29.3 + - + +
510B VAL* 3.8 29.6 - - + -
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Residues in contact with ARG 403 (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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402B ILE* 1.3 88.7 - - - +
404B GLY* 1.3 63.0 + - - +
405B ASP* 3.3 11.9 - - - +
406B GLU* 3.3 48.5 + - - +
407B VAL* 3.9 2.4 + - - +
417B LYS* 4.1 9.7 - - - +
453B TYR* 4.7 9.7 + - - -
495B TYR* 3.7 43.2 + - + +
496B GLY 5.7 1.4 - - - +
497B PHE* 4.5 5.3 - - + -
504B GLY 3.1 22.7 - - - +
505B TYR* 3.2 43.3 + - - +
506B GLN 3.8 4.7 - - - -
508B TYR* 4.7 0.4 - - - -
373C SER* 3.9 17.0 + - - -
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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