Contacts of the strand formed by residues 506 - 515 (chain B) in PDB entry 5ZHU
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 GLN 506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B GLU* 5.7 0.7 - - - +
501B ALA 3.8 0.5 - - - +
502B HIS* 3.4 7.3 + - - -
503B ALA 2.8 30.7 + - - +
504B GLN* 4.1 4.9 + - - +
505B ASN* 1.3 85.7 + - - +
507B ASN* 1.3 70.3 + - - +
508B TYR* 3.3 32.8 + - + +
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Residues in contact with ASN 507 (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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421B TYR* 3.4 23.5 - - - -
500B GLN* 3.6 31.4 + - + +
501B ALA 3.4 3.1 - - - +
502B HIS* 3.2 25.5 + - - +
506B GLN* 1.3 80.9 - - - +
508B TYR* 1.3 71.9 + - - +
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Residues in contact with TYR 508 (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 ALA* 3.8 23.6 - - + +
408B VAL* 4.1 8.3 - - + -
410B THR* 3.4 42.3 - - + +
411B PRO* 4.4 12.1 - - + -
412B GLU* 4.5 4.3 + - - -
500B GLN* 3.3 3.7 - - - -
501B ALA* 2.8 48.0 + - + +
503B ALA* 3.7 24.6 + - + -
504B GLN* 3.9 15.9 + - - -
506B GLN* 3.3 35.4 + - + +
507B ASN* 1.3 79.1 - - - +
509B THR* 1.3 63.9 + - - +
510B LEU* 3.3 2.6 + - - +
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Residues in contact with THR 509 (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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351B LYS 4.6 3.7 + - - +
352B TRP* 3.2 34.2 - - + +
353B ALA 2.9 26.0 + - - +
498B ALA* 4.4 6.7 - - + +
499B LEU 3.5 7.2 - - - +
500B GLN* 4.2 16.8 + - - +
507B ASN 4.5 0.2 + - - -
508B TYR* 1.3 69.8 - - - +
510B LEU* 1.3 60.6 + - - +
511B ALA 3.6 20.6 - - - +
512B ALA* 3.8 10.3 - - + -
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Residues in contact with LEU 510 (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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352B TRP* 3.3 21.2 - - - +
353B ALA* 3.5 33.6 - - + +
354B THR 4.5 0.2 - - - +
355B LEU* 3.8 28.9 - - + -
365B MET* 3.4 11.5 - - - +
366B LEU* 4.4 11.9 - - + -
408B VAL* 5.0 0.7 - - + -
420B PHE* 3.7 24.7 - - + -
499B LEU* 2.9 24.5 + - + +
501B ALA* 3.6 38.1 - - + +
508B TYR 3.9 5.6 - - - +
509B THR* 1.3 73.3 - - - +
511B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 511 (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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352B TRP* 3.8 13.2 - - + -
365B MET* 4.1 13.7 - - + -
366B LEU* 4.2 7.9 - - + -
368B TYR* 3.7 34.3 - - + -
498B ALA* 3.4 0.5 - - - -
499B LEU* 2.8 31.5 + - + +
509B THR* 3.5 4.3 - - - +
510B LEU* 1.3 81.5 - - - +
512B ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 512 (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 PRO* 3.4 4.3 - - - +
347B HIS* 2.9 45.2 + - + +
352B TRP* 3.2 13.4 - - - -
368B TYR* 4.0 1.3 - - - -
496B VAL* 4.8 5.8 - - + -
497B VAL 3.3 7.2 - - - +
498B ALA* 3.8 18.4 - - + -
509B THR* 3.8 10.1 - - + -
511B ALA* 1.3 77.3 - - - +
513B GLN* 1.3 65.0 + - - +
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Residues in contact with GLN 513 (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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344B TRP* 3.4 36.3 - - + +
345B GLN* 3.2 9.3 - - - +
346B PRO* 3.3 39.0 - - - +
347B HIS* 4.2 3.4 - - - +
352B TRP* 5.6 1.8 - - - -
368B TYR* 3.6 31.3 + - + +
369B ARG* 5.3 0.3 - - - -
370B VAL* 3.8 19.8 + - + +
495B LEU 3.8 0.7 - - - +
496B VAL* 3.4 3.8 - - - +
497B VAL 2.9 30.9 + - - -
512B ALA* 1.3 75.5 + - - +
514B ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 514 (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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344B TRP* 3.4 4.7 - - - -
345B GLN* 2.9 52.4 + - + +
346B PRO 4.4 0.4 - - - +
347B HIS* 3.8 38.1 - - + +
427B VAL* 4.0 9.4 - - + -
432B LEU* 5.1 4.3 - - + -
494B MET* 3.6 34.5 - - + -
495B LEU 3.2 10.3 - - - +
496B VAL* 3.8 17.3 - - + -
513B GLN* 1.3 73.2 - - - +
515B SER* 1.3 72.4 + - - +
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Residues in contact with SER 515 (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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342B ILE* 4.0 12.8 - - - -
343B LYS 3.3 11.2 - - - -
344B TRP* 3.3 27.3 - - - -
494B MET* 3.1 28.1 - - - +
495B LEU* 2.8 30.2 + - - -
514B ILE* 1.3 75.6 - - - +
516B GLU* 1.3 73.0 + - - +
518B ILE* 3.4 8.1 - - - +
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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