Contacts of the strand formed by residues 367 - 375 (chain B) in PDB entry 1YQZ
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 PRO 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B TYR* 5.5 5.3 - - + +
354B THR* 4.1 20.2 - - + -
355B GLN* 3.7 11.2 - - - +
356B GLY* 4.3 1.1 - - - -
365B ASN 4.9 0.2 - - - +
366B SER* 1.3 85.6 - - - +
368B LEU* 1.3 59.1 + - - +
369B HIS* 4.1 0.9 + - - +
387B VAL 4.2 0.5 - - - +
388B GLY* 3.9 15.0 - - - -
389B LYS* 4.6 2.4 + - + -
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B THR* 3.3 4.2 - - - -
355B GLN 2.8 36.9 + - - +
357B ALA* 4.4 9.9 - - + -
366B SER 3.4 0.8 + - - -
367B PRO* 1.3 73.4 - - - +
369B HIS* 1.3 62.5 + - - +
370B LEU* 5.3 0.2 - - + -
386B ALA* 4.3 3.4 - - + -
387B VAL 3.6 22.4 - - - +
388B GLY* 4.0 2.0 - - - +
390B GLU 3.6 26.0 - - - +
391B GLY 3.6 17.7 - - - +
392B ALA* 3.7 24.0 - - + -
395B ARG* 3.7 28.0 - - + +
429B LEU* 3.4 22.1 - - + +
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Residues in contact with HIS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 5.6 1.1 - - - -
191B MET* 3.7 30.4 - - + +
352B GLU* 2.7 34.7 + - + +
353B VAL 3.6 6.5 - - - -
354B THR* 3.5 23.8 - - + +
367B PRO 4.1 1.0 + - - -
368B LEU* 1.3 72.9 - - - +
370B LEU* 1.3 69.9 + - - +
371B ARG* 3.5 19.3 + - - +
385B ALA 3.8 0.9 - - - +
386B ALA* 3.1 6.9 - - - +
387B VAL* 2.9 37.7 + - + +
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU* 3.2 3.5 - - - +
353B VAL* 2.9 42.3 + - + +
368B LEU* 3.9 1.9 + - + -
369B HIS* 1.3 75.2 - - - +
371B ARG* 1.3 64.6 - - - +
372B VAL* 4.5 1.8 - - + -
385B ALA 3.5 15.3 - - - +
386B ALA* 4.0 14.1 - - + -
395B ARG* 4.4 9.9 - - + -
396B ILE* 4.3 3.1 - - + -
399B LEU* 3.8 23.6 - - + -
429B LEU* 4.0 28.3 - - + -
430B ILE* 4.0 22.2 - - + -
433B ILE* 3.7 27.3 - - + +
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASP* 2.9 28.1 + - - +
190B ASP* 2.7 44.1 + - - -
191B MET* 3.5 20.7 - - - -
350B MET* 3.6 31.2 - - + +
351B VAL 3.5 3.6 - - - -
352B GLU* 2.9 32.5 + - + -
369B HIS* 3.5 13.0 - - - +
370B LEU* 1.3 75.7 - - - +
372B VAL* 1.3 67.9 + - - +
373B TYR* 3.5 20.6 + - + -
384B ALA* 3.2 5.2 - - - +
385B ALA* 2.8 38.0 + - + +
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LYS 4.0 0.5 - - - +
350B MET* 3.5 1.6 - - - +
351B VAL* 2.9 37.0 + - + +
370B LEU* 4.5 1.8 - - + -
371B ARG* 1.3 80.8 - - - +
373B TYR* 1.3 76.4 + - - +
374B TYR* 4.7 0.4 - - + -
381B ILE* 3.9 23.8 - - + -
383B ARG 3.5 6.5 - - - +
384B ALA* 4.0 13.9 - - + -
399B LEU* 4.1 18.2 - - + -
409B VAL* 4.3 9.2 - - + -
412B LEU* 4.9 1.3 - - + -
433B ILE* 3.8 39.7 - - + -
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Residues in contact with TYR 373 (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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188B ASP* 2.6 32.1 + - - -
343B LEU* 3.6 35.6 - - + +
348B TYR* 3.7 31.9 - + + -
349B LYS 3.3 5.2 - - - +
350B MET* 3.8 20.3 - - + +
371B ARG* 3.5 24.9 + - + -
372B VAL* 1.3 76.8 - - - +
374B TYR* 1.3 63.1 + - - +
381B ILE* 3.7 2.8 - - - -
382B LEU* 2.8 25.4 + - + -
383B ARG* 2.8 46.3 + - + +
385B ALA* 5.7 1.6 - - + -
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Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B TYR* 3.2 5.4 - - - +
349B LYS* 2.9 75.4 + - + +
351B VAL* 3.5 28.6 - - + +
372B VAL 4.7 1.8 - - - -
373B TYR* 1.3 75.6 - - - +
375B ASP* 1.3 73.6 + - - +
376B THR* 4.6 4.9 - - + -
379B ARG* 3.3 40.1 + - - +
380B GLN 3.2 15.5 - - - +
381B ILE* 4.3 1.8 - - + -
382B LEU* 3.7 6.1 - - - +
409B VAL* 3.7 40.2 - - + -
437B ALA* 4.2 2.3 - - + -
438B LYS* 3.5 14.4 + - - -
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Residues in contact with ASP 375 (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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346B PHE* 3.7 23.8 - - - -
347B ASP* 3.6 13.2 + - - +
374B TYR* 1.3 71.3 - - - +
376B THR* 1.3 59.7 + - - +
377B SER* 2.6 44.4 + - - -
378B ASN* 3.2 23.3 + - - +
379B ARG* 2.8 30.7 + - - -
380B GLN* 2.8 14.7 + - + +
382B LEU* 3.5 15.8 - - + +
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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