Contacts of the strand formed by residues 703 - 712 (chain A) in PDB entry 1DQ8
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 GLY 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A ALA* 3.8 1.7 - - - +
586A ASP* 3.3 4.7 - - - -
587A GLY 2.8 43.5 + - - +
588A MET* 4.1 16.5 - - - +
648A GLN* 5.1 0.7 + - - -
702A ARG* 1.3 77.0 + - - +
704A LYS* 1.3 68.5 + - - -
705A SER* 4.0 0.9 + - - -
800A ILE 3.6 7.4 - - - -
801A GLU* 4.6 0.9 - - - -
802A ILE 5.5 0.7 - - - -
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Residues in contact with LYS 704 (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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583A VAL* 4.6 8.5 - - + -
585A ALA 3.5 8.5 - - - +
586A ASP* 3.1 35.8 + - - +
651A SER* 5.1 2.6 + - - -
652A GLY 4.7 6.3 + - - -
654A ALA 4.8 5.1 + - - -
655A MET 5.8 0.8 + - - -
702A ARG 3.2 0.4 + - - -
703A GLY* 1.3 75.7 - - - -
705A SER* 1.3 60.0 + - - +
706A VAL* 3.9 4.9 + - + -
797A MET 3.6 5.0 - - - +
798A PRO 4.1 1.3 - - - -
799A SER 3.6 1.4 + - - -
800A ILE* 2.8 47.0 + - + +
802A ILE* 4.0 19.6 + - + +
832A GLY 4.9 0.2 - - - -
835A ALA* 3.9 29.0 - - - +
836A ARG* 4.1 16.2 - - - +
839A ALA* 3.7 27.4 - - + -
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Residues in contact with SER 705 (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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583A VAL* 3.4 5.4 - - - +
584A LEU* 2.7 41.4 + - - -
585A ALA* 3.0 33.1 + - - +
700A GLU 5.1 0.3 + - - -
701A GLY* 3.9 10.9 - - - -
702A ARG 4.6 0.7 + - - -
703A GLY 4.0 0.9 + - - -
704A LYS* 1.3 71.5 - - - +
706A VAL* 1.3 56.2 + - - +
797A MET 3.4 5.2 - - - -
798A PRO* 2.7 27.8 + - - +
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Residues in contact with VAL 706 (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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581A SER* 4.5 2.2 - - - -
582A ARG 3.3 15.7 - - - +
583A VAL* 4.2 9.4 - - + -
584A LEU* 4.2 4.2 - - - +
704A LYS* 4.1 8.1 - - + -
705A SER* 1.3 80.7 - - - +
707A VAL* 1.3 71.5 + - - +
796A THR* 3.5 3.3 - - - +
797A MET 2.8 35.0 + - - +
800A ILE* 4.2 6.3 - - + -
839A ALA* 3.8 32.3 - - + +
840A ARG* 4.1 15.5 - - + -
843A CYS* 3.6 28.5 - - + -
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Residues in contact with VAL 707 (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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581A SER* 3.2 6.6 - - - -
582A ARG* 3.0 52.6 + - + +
584A LEU* 4.0 23.3 - - + -
706A VAL* 1.3 76.6 - - - +
708A CYS* 1.3 65.0 + - - +
795A CYS 3.5 4.9 - - - +
796A THR* 3.5 21.1 - - + +
843A CYS* 4.2 0.2 - - - -
599D ALA* 3.8 35.4 - - + +
638D ILE* 4.1 7.9 - - + -
640D GLY* 3.9 11.7 - - - +
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Residues in contact with CYS 708 (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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546A LEU* 4.0 16.6 - - - -
579A ALA* 4.2 1.6 - - - -
580A SER 3.4 13.2 - - - -
581A SER* 4.1 4.3 - - - -
707A VAL* 1.3 78.7 - - - +
709A GLU* 1.3 68.8 + - - +
794A SER* 3.1 25.6 - - - -
795A CYS 2.9 10.3 + - - +
843A CYS* 3.8 22.7 - - - +
844A GLY* 3.7 25.4 - - - -
847A MET* 3.8 22.9 - - + -
599D ALA* 5.1 0.7 - - - -
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Residues in contact with GLU 709 (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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579A ALA* 3.2 4.2 - - - +
580A SER* 2.9 43.7 + - - +
708A CYS* 1.3 79.7 - - - +
710A ALA* 1.3 66.2 + - - +
792A TYR* 2.8 35.0 + - + +
793A ILE 3.2 12.3 - - - +
847A MET* 3.6 5.2 - - - -
598D ARG* 3.6 15.4 - - - +
599D ALA* 2.7 29.7 + - + -
600D CYS* 3.0 36.4 + - - -
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Residues in contact with ALA 710 (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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573A ILE* 4.6 5.6 - - + +
578A GLY 4.1 17.0 - - - +
579A ALA* 4.1 3.4 - - + -
709A GLU* 1.3 79.9 - - - +
711A VAL* 1.3 65.7 + - - +
712A ILE* 4.2 15.7 - - + -
792A TYR* 3.6 3.9 - - - -
793A ILE* 2.9 36.4 + - + +
847A MET* 3.5 18.4 - - + -
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Residues in contact with VAL 711 (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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576A GLY* 3.4 22.2 + - - +
578A GLY 5.0 1.8 + - - -
710A ALA* 1.3 79.7 - - - +
712A ILE* 1.3 68.7 + - - +
713A PRO* 3.7 5.1 - - + +
784A SER* 4.2 17.3 - - - +
785A GLY 5.8 0.2 - - - +
790A ASP* 4.0 26.5 - - + -
791A LEU 3.2 5.8 - - - +
792A TYR* 3.9 21.1 - - + -
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Residues in contact with ILE 712 (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 ALA* 3.7 23.3 - - + +
573A ILE* 3.9 13.7 - - + -
710A ALA* 4.3 9.2 - - + -
711A VAL* 1.3 82.4 - - - +
713A PRO* 1.3 71.2 - - + +
716A VAL* 3.9 22.4 - - + -
717A VAL* 3.5 25.5 - - + +
721A LEU* 4.4 3.4 - - + -
790A ASP* 3.6 0.7 - - - -
791A LEU* 2.8 46.7 + - + +
793A ILE* 4.8 3.4 - - + -
851A LEU* 3.8 39.3 - - + -
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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