Contacts of the strand formed by residues 566 - 574 (chain A) in PDB entry 1Q6S
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 TYR 566 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534A VAL* 3.9 18.4 - - + -
535A ALA* 3.3 24.4 - - + +
540A ASN* 3.5 31.9 - - + +
543A ARG* 2.8 47.1 + - + -
544A ASN* 2.5 31.8 + - - -
551A PRO* 3.2 29.2 - - + +
556A ARG* 4.0 10.3 - - - +
559A LEU* 3.6 3.5 - - - +
564A ASN* 3.0 18.2 + - - +
565A ASP* 1.3 83.6 + - - +
567A ILE* 1.3 73.7 + - - +
568A ASN* 3.5 16.9 - - - -
594A HIS* 4.9 1.7 - - - -
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Residues in contact with ILE 567 (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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543A ARG* 5.5 2.2 - - - +
551A PRO* 4.2 1.6 - - - +
556A ARG* 5.0 0.7 - - - +
557A ILE* 3.4 27.8 + - + +
559A LEU* 3.9 21.3 - - + -
565A ASP 3.8 0.2 + - - -
566A TYR* 1.3 93.6 - - - +
568A ASN* 1.3 69.1 + - - +
569A ALA* 2.8 21.8 + - + +
584A THR* 4.4 5.2 - - - +
585A GLN* 6.1 1.8 - - + +
591A THR* 5.1 7.9 - - + +
594A HIS* 3.9 27.8 - - + +
595A PHE* 4.0 13.7 - - + +
598A MET* 3.8 26.9 - - + -
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Residues in contact with ASN 568 (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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543A ARG 4.1 3.7 + - - +
544A ASN* 3.0 19.6 + - - +
545A ARG 5.0 0.2 - - - +
546A TYR 5.7 0.2 - - - +
549A VAL* 2.9 28.9 + - - +
550A SER 4.5 0.2 - - - -
551A PRO* 3.6 12.1 - - - +
566A TYR* 3.5 16.8 + - - +
567A ILE* 1.3 73.1 - - - +
569A ALA* 1.3 52.5 + - - +
584A THR* 2.6 29.3 + - - -
585A GLN* 3.4 36.0 + - - +
757A ARG* 2.9 31.1 + - - +
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Residues in contact with ALA 569 (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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551A PRO* 3.5 6.7 - - - +
556A ARG* 3.3 7.4 - - - +
557A ILE* 3.0 29.8 + - + -
567A ILE* 2.8 9.5 + - + +
568A ASN* 1.3 76.6 + - - +
570A SER* 1.3 63.6 + - - +
582A ILE* 4.2 1.6 - - + -
583A LEU 3.2 8.5 - - - +
584A THR* 3.5 13.7 - - - +
598A MET* 3.5 32.5 - - + -
757A ARG* 4.0 1.3 - - - +
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Residues in contact with SER 570 (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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551A PRO* 3.3 17.0 - - - +
552A PHE 4.4 0.3 + - - -
555A SER* 3.4 9.0 - - - -
557A ILE* 4.1 4.9 - - - -
569A ALA* 1.3 73.2 - - - +
571A LEU* 1.3 61.7 + - - +
572A ILE* 3.7 10.8 - - - +
582A ILE* 3.2 4.7 - - - -
583A LEU 2.8 30.6 + - - -
756A PHE 3.5 21.3 + - - -
757A ARG* 3.0 31.9 + - - +
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Residues in contact with LEU 571 (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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555A SER* 2.7 24.5 + - - +
557A ILE* 3.7 16.7 - - + +
570A SER* 1.3 72.6 - - - +
572A ILE* 1.3 63.0 + - - +
573A LYS* 4.7 16.8 - - + +
580A SER* 4.1 22.9 - - - -
581A TYR 3.6 11.9 - - - +
582A ILE* 4.2 3.1 - - + +
710A PRO* 4.2 18.8 - - + -
756A PHE* 3.5 22.5 - - - +
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Residues in contact with ILE 572 (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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570A SER* 3.7 24.7 - - - +
571A LEU* 1.3 80.4 - - - +
573A LYS* 1.3 59.3 + - - +
574A MET* 3.9 24.6 + - - -
580A SER* 3.2 4.9 - - - -
581A TYR* 2.7 56.4 + - + +
583A LEU* 4.1 20.4 - - + -
726A CYS* 5.9 0.4 - - + -
753A MET* 4.4 17.5 - - + +
756A PHE* 3.7 24.2 - - + -
757A ARG* 4.0 10.3 - - + -
760A LEU* 4.6 9.4 - - + -
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Residues in contact with LYS 573 (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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571A LEU* 3.9 20.3 + - + -
572A ILE* 1.3 75.1 - - - +
574A MET* 1.3 65.8 + - - +
575A GLU* 3.5 31.4 + - - +
579A ARG 4.9 0.7 - - - +
580A SER* 3.5 19.7 - - - +
752A GLU* 5.0 1.0 - - - +
756A PHE* 3.4 35.4 - - + -
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Residues in contact with MET 574 (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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572A ILE* 3.9 15.7 - - + -
573A LYS* 1.3 78.2 - - - +
575A GLU* 1.3 58.9 + - - +
576A GLU 3.7 1.1 - - - -
577A ALA* 4.0 17.3 - - + -
578A GLN* 2.9 25.3 + - - -
579A ARG* 3.0 23.0 + - + +
581A TYR* 4.2 2.0 - - + -
730A THR* 3.7 22.7 - - + +
734A LEU* 6.0 1.1 - - + -
749A VAL* 3.8 21.1 - - + -
752A GLU* 3.8 27.1 - - + -
753A MET* 3.8 36.1 - - + -
756A PHE* 4.7 1.6 - - - -
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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