Contacts of the strand formed by residues 653 - 662 (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 653 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A LYS* 2.9 70.3 + - + +
651A SER 3.6 1.2 - - - -
652A TYR* 1.3 88.1 - + + +
654A THR* 1.3 63.7 + - - +
655A VAL* 3.5 29.8 - - + -
675A HIS 3.0 16.6 - - - +
676A TYR* 3.7 4.0 - + + -
677A THR* 3.8 6.0 + - - -
690A SER 5.2 2.0 - - - -
693A ASN* 3.6 28.8 + - - -
694A PHE* 3.7 37.9 - + + -
697A LYS* 3.9 29.7 - - + +
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Residues in contact with THR 654 (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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647A GLU* 4.1 2.9 - - + +
648A ASP 3.4 13.0 - - - +
649A ILE* 3.7 34.9 - - + +
650A LYS 4.6 0.5 + - - -
653A TYR* 1.3 75.8 + - - +
655A VAL* 1.3 67.5 + - - +
656A ARG* 3.7 43.5 + - + +
673A HIS 3.5 1.2 - - - +
674A PHE* 3.8 0.5 - - - -
675A HIS* 2.7 39.6 + - - +
677A THR* 4.4 9.9 + - - +
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Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A GLU* 3.2 1.6 - - - -
648A ASP* 2.7 48.7 + - + +
650A LYS* 6.0 0.2 - - + -
653A TYR* 3.5 31.4 - - + -
654A THR* 1.3 74.7 - - - +
656A ARG* 1.3 68.5 + - - +
657A GLN 4.4 0.2 + - - -
672A LEU* 5.3 6.5 - - + -
673A HIS 3.3 8.7 - - - +
674A PHE* 4.0 35.2 - - + -
697A LYS* 4.5 11.7 - - + -
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Residues in contact with ARG 656 (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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625A TRP* 3.3 40.7 - - - +
627A GLN* 6.2 0.2 - - - +
644A LEU* 4.5 7.2 - - + -
646A SER 3.4 8.3 - - - +
647A GLU* 3.1 30.2 + - + -
649A ILE* 6.2 0.4 - - - +
654A THR* 3.7 20.5 + - + +
655A VAL* 1.3 80.7 - - - +
657A GLN* 1.3 60.8 + - - +
658A LEU* 3.9 9.2 - - + -
671A ILE 3.8 0.3 - - - +
672A LEU* 3.5 7.2 - - - +
673A HIS* 2.8 72.2 + - + +
675A HIS* 3.3 35.8 + - - +
677A THR* 5.5 1.4 - - - +
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Residues in contact with GLN 657 (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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644A LEU* 3.6 2.9 - - - +
645A ILE* 2.8 49.4 + - + +
646A SER* 2.8 32.4 + - - +
655A VAL 4.4 0.2 + - - -
656A ARG* 1.3 72.3 - - - +
658A LEU* 1.3 60.2 + - - +
670A GLU* 2.6 36.9 + - + +
671A ILE 4.0 2.0 - - - -
672A LEU* 4.4 8.1 - - + -
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Residues in contact with LEU 658 (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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596A TRP* 3.9 29.6 - - + -
625A TRP* 4.4 12.6 - - + -
626A PRO* 4.6 11.9 - - + -
642A LEU* 4.0 12.1 - - + -
643A THR 3.4 5.2 - - - +
644A LEU* 3.8 29.4 - - + +
645A ILE* 4.1 3.6 - - - -
656A ARG* 4.4 7.2 - - + -
657A GLN* 1.3 81.2 - - - +
659A GLU* 1.3 61.7 + - - +
670A GLU* 3.2 9.5 - - - +
671A ILE* 2.7 43.8 + - + +
673A HIS* 3.9 29.6 - - + -
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Residues in contact with GLU 659 (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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641A LYS 3.7 1.2 - - - +
642A LEU* 3.5 5.9 - - - +
643A THR* 2.9 39.5 + - - +
645A ILE* 3.9 27.2 - - + +
658A LEU* 1.3 74.6 - - - +
660A LEU* 1.3 62.4 + - - +
661A GLU* 4.0 6.0 + - + +
668A THR* 4.0 30.3 + - + +
669A ARG 3.5 8.7 - - - +
670A GLU* 4.6 1.1 - - - +
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Residues in contact with LEU 660 (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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596A TRP* 3.9 36.8 - - + +
599A VAL* 3.9 29.2 - - + -
600A TRP* 3.4 29.8 - - + -
635A PHE* 5.7 0.4 - - + -
640A LEU* 4.3 15.9 - - + -
641A LYS 3.6 9.2 - - - +
642A LEU* 4.0 14.8 - - + -
658A LEU 4.0 0.8 - - - -
659A GLU* 1.3 72.4 - - - +
661A GLU* 1.3 63.4 + - - +
668A THR* 3.3 2.6 - - - -
669A ARG 2.8 34.8 + - - +
671A ILE* 3.7 21.1 - - + +
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Residues in contact with GLU 661 (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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600A TRP* 4.4 0.4 - - - -
640A LEU* 3.3 8.2 - - - +
641A LYS* 2.8 66.1 + - + +
659A GLU* 4.0 7.1 + - + +
660A LEU* 1.3 75.1 - - - +
662A ASN* 1.3 66.9 + - - +
663A LEU* 3.3 25.1 + - + +
666A GLN* 4.7 12.6 + - - +
667A GLU 3.2 10.1 - - - +
668A THR* 3.6 21.9 - - + +
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Residues in contact with ASN 662 (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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600A TRP* 3.4 44.3 - - + +
638A THR 5.4 0.7 - - - +
639A ASN 4.1 1.7 - - - +
640A LEU* 3.6 17.1 - - + +
661A GLU* 1.3 71.9 - - - +
663A LEU* 1.3 52.5 + - - +
664A THR* 2.8 35.5 + - - -
665A THR* 3.1 32.4 + - - +
666A GLN* 2.7 36.9 + - - -
667A GLU 2.8 8.3 + - - +
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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