Contacts of the strand formed by residues 576 - 586 (chain A) in PDB entry 2ZB5
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 LYS 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ARG 5.3 1.6 + - - -
197A GLN* 2.6 42.8 + - - +
572A THR* 3.1 7.6 - - - -
573A TRP 2.9 27.7 + - - +
574A ASP* 3.8 8.5 - - + +
575A GLN* 1.3 84.0 - - - +
577A LEU* 1.3 61.3 + - - +
578A TRP* 3.6 24.4 + - + +
601A GLY 3.7 17.7 + - - +
602A MET 3.4 13.7 - - - +
603A GLY* 4.0 13.0 - - - -
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU* 3.6 41.5 - - + -
525A VAL* 4.1 14.8 - - + -
542A VAL* 4.3 12.6 - - + -
549A PHE* 5.6 4.7 - - + -
570A CYS* 4.0 1.1 - - + -
571A PHE 3.8 19.7 - - - +
572A THR* 4.3 9.0 - - + +
576A LYS* 1.3 70.3 - - - +
578A TRP* 1.3 61.7 + - - +
579A CYS* 3.5 25.1 - - - -
602A MET* 3.0 48.0 + - + +
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Residues in contact with TRP 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLN* 3.1 54.1 - - + -
198A PHE 4.7 0.2 - - - -
199A SER* 4.3 16.8 - - - -
266A GLY 4.7 0.2 - - - -
267A ALA* 3.9 10.1 - - + -
268A PRO* 3.5 26.5 - - + -
570A CYS* 3.1 3.1 - - - +
571A PHE* 2.9 58.5 + - + +
573A TRP* 3.3 46.6 + + + -
576A LYS* 3.6 18.8 - - + +
577A LEU* 1.3 72.8 - - - +
579A CYS* 1.3 60.2 + - - +
599A MET* 4.0 13.9 - - + -
600A VAL* 3.2 10.5 - - - -
601A GLY* 3.4 28.0 - - - -
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Residues in contact with CYS 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A VAL* 4.1 0.9 - - - -
540A TYR* 3.4 32.9 + - + +
568A VAL* 4.7 0.4 - - + -
569A GLU 3.3 4.3 - - - -
570A CYS* 2.0 45.3 - - - -
571A PHE* 5.3 1.1 - - - -
577A LEU* 3.5 22.4 + - - -
578A TRP* 1.3 73.1 - - - +
580A ARG* 1.3 60.7 + - - +
598A GLY 3.9 0.5 - - - +
599A MET* 3.1 5.9 - - - +
600A VAL* 2.9 32.2 + - - +
602A MET* 3.5 12.3 - - + -
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Residues in contact with ARG 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A SER 4.5 7.5 + - - -
200A ASN* 5.0 9.3 + - - +
201A MET 5.5 2.2 + - - -
202A SER* 4.9 4.9 - - - -
207A ASP* 3.3 32.0 + - - -
270A PHE* 5.0 6.0 - - + -
540A TYR* 4.0 1.1 - - - -
568A VAL* 3.6 1.2 - - - +
569A GLU* 2.9 46.9 + - + +
571A PHE* 5.6 0.9 - - + -
579A CYS* 1.3 74.2 - - - +
581A HIS* 1.3 62.0 + - - +
582A PHE* 3.5 31.5 - - + -
597A SER* 3.3 22.0 + - - -
598A GLY* 3.2 12.7 + - - +
599A MET* 3.2 57.7 - - + +
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Residues in contact with HIS 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A ALA* 5.6 0.4 - - + -
538A VAL* 4.0 21.9 - - + +
540A TYR* 3.0 26.4 + - + +
553A TYR* 3.7 39.2 - + - -
566A LEU* 4.7 4.7 - - + -
567A GLN 3.3 13.0 - - - +
568A VAL* 3.6 8.1 - - + -
580A ARG* 1.3 73.8 - - - +
582A PHE* 1.3 68.2 + - - +
583A CYS* 4.3 11.0 - - + -
596A HIS* 3.3 33.6 + - - -
597A SER* 3.2 29.8 + - - -
598A GLY 2.9 19.8 + - - -
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Residues in contact with PHE 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.8 23.8 - - + -
207A ASP* 4.8 2.7 - - - -
210A LEU* 3.6 33.4 - - + -
219A ILE* 3.8 21.1 - - + -
221A THR* 3.7 14.1 - - - -
565A GLU* 3.8 2.1 - - - +
566A LEU* 3.7 2.3 - - - -
567A GLN* 2.9 50.1 + - + +
568A VAL* 5.4 0.4 - - - -
569A GLU* 3.4 25.4 - - + -
580A ARG* 3.5 30.3 - - + -
581A HIS* 1.3 79.6 - - - +
583A CYS* 1.3 62.0 + - - +
584A VAL* 4.0 4.6 + - + +
595A THR* 4.5 5.4 - - + -
596A HIS 3.5 5.2 - - - -
597A SER* 3.7 8.3 - - - -
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Residues in contact with CYS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR* 3.7 37.9 - - - -
538A VAL* 4.9 4.5 - - + -
563A PRO* 4.8 3.8 - - - -
565A GLU 3.4 6.1 - - - -
566A LEU* 3.8 21.5 - - + -
581A HIS* 4.1 7.8 - - + -
582A PHE* 1.3 73.4 - - - +
584A VAL* 1.3 63.5 + - - +
585A LEU* 3.6 15.9 + - + +
594A ILE 3.7 0.3 - - - +
595A THR* 3.6 2.0 - - - +
596A HIS* 2.8 46.5 + - + +
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Residues in contact with VAL 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL 6.0 0.4 - - - +
217A SER* 6.5 1.3 - - - -
218A SER 6.4 0.2 - - - +
219A ILE* 6.0 3.8 - - + -
563A PRO* 3.7 2.3 - - - +
564A ILE* 2.8 50.3 + - + +
565A GLU* 2.7 47.7 + - + +
582A PHE* 5.0 4.9 - - + +
583A CYS* 1.3 72.3 - - - +
585A LEU* 1.3 68.1 + - - +
593A HIS* 4.3 14.8 - - + +
594A ILE 3.7 5.2 - - - +
595A THR* 3.8 22.2 - - + +
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Residues in contact with LEU 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR* 3.6 33.7 - - + +
558A PRO* 4.2 30.7 - - + +
561A GLY* 4.2 13.0 - - - +
562A VAL 3.2 10.3 - - - +
563A PRO* 3.5 31.6 - - + -
583A CYS* 4.3 12.8 - - - +
584A VAL* 1.3 77.0 - - - +
586A ALA* 1.3 60.4 + - - +
593A HIS* 3.3 4.5 - - - +
594A ILE* 2.7 58.0 + - + +
596A HIS* 5.2 7.0 - - + -
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Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A GLY* 4.3 0.9 - - - -
562A VAL* 2.7 47.2 + - + +
564A ILE* 3.9 21.5 - - + -
584A VAL 4.4 0.2 + - - -
585A LEU* 1.3 76.2 - - - +
587A ASP* 1.3 59.9 + - - +
592A GLY 3.1 12.1 - - - +
593A HIS* 3.9 17.5 - - + +
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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