Contacts of the strand formed by residues 703 - 712 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585D ALA* 3.7 1.7 - - - +
586D ASP* 3.2 5.3 + - - -
587D GLY 2.8 42.9 + - - +
588D MET* 4.0 18.5 - - - +
648D GLN* 5.0 0.9 + - - -
702D ARG* 1.3 77.2 + - - +
704D LYS* 1.3 68.4 + - - -
705D SER* 4.1 0.7 + - - -
800D ILE 3.5 8.3 - - - -
801D GLU* 4.6 0.7 - - - -
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Residues in contact with LYS 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D VAL* 4.5 10.8 - - + -
585D ALA 3.4 8.7 - - - +
586D ASP* 3.0 35.2 + - - +
651D SER* 5.3 2.4 + - - -
652D GLY 4.7 6.5 + - - -
654D ALA 4.8 5.1 + - - -
655D MET 5.7 1.2 + - - -
702D ARG 3.2 0.6 + - - -
703D GLY* 1.3 75.6 - - - -
705D SER* 1.3 60.9 + - - +
706D VAL* 3.8 5.0 + - + +
797D MET 3.4 5.2 - - - +
798D PRO 3.7 1.9 - - - -
800D ILE* 2.7 45.4 + - - +
802D ILE* 3.9 16.9 + - + +
832D GLY 4.9 0.2 - - - -
835D ALA* 3.9 26.5 - - - +
836D ARG* 4.0 17.7 - - - +
839D ALA* 3.7 27.8 - - + -
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Residues in contact with SER 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LYS* 6.3 0.2 - - - -
583D VAL* 3.5 2.3 - - - -
584D LEU* 2.7 43.3 + - - -
585D ALA* 3.0 31.1 + - - +
700D GLU 5.1 0.2 + - - -
701D GLY* 3.8 11.4 - - - -
702D ARG 4.5 0.7 + - - -
703D GLY 4.1 0.9 + - - -
704D LYS* 1.3 70.4 - - - +
706D VAL* 1.3 59.2 + - - +
797D MET 3.4 5.8 - - - -
798D PRO* 2.6 27.9 + - - +
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Residues in contact with VAL 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D SER* 4.7 1.3 - - - -
582D ARG 3.4 15.3 - - - +
583D VAL* 4.5 9.0 - - + -
584D LEU* 4.3 4.2 - - - +
704D LYS* 4.0 9.4 - - + -
705D SER* 1.3 81.1 - - - +
707D VAL* 1.3 68.7 + - - +
796D THR* 3.5 5.2 - - - +
797D MET 2.8 37.7 + - - +
800D ILE* 4.0 9.2 - - + -
839D ALA* 3.9 27.8 - - + -
840D ARG* 4.2 15.3 - - + -
843D CYS* 3.6 29.3 - - + -
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Residues in contact with VAL 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A ALA* 3.8 27.4 - - + +
638A ILE* 4.2 4.9 - - + -
640A GLY* 3.7 21.8 - - - +
581D SER* 3.1 5.6 - - - -
582D ARG* 3.0 45.1 + - + +
584D LEU* 4.1 25.6 - - + -
706D VAL* 1.3 78.6 - - - +
708D CYS* 1.3 65.8 + - - +
795D CYS 3.4 5.8 - - - +
796D THR* 3.3 23.6 - - - +
843D CYS* 4.2 0.2 - - - -
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Residues in contact with CYS 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A ALA* 5.3 0.4 - - - -
546D LEU* 3.7 26.2 - - - -
579D ALA* 4.1 1.3 - - - -
580D SER 3.3 13.0 - - - -
581D SER* 3.8 5.2 - - - -
707D VAL* 1.3 76.7 - - - +
709D GLU* 1.3 71.7 + - - +
794D SER* 3.2 6.6 - - - -
795D CYS 2.9 30.0 + - - +
843D CYS* 3.8 22.7 - - - +
844D GLY* 3.7 12.6 - - - +
847D MET* 3.7 26.2 - - + -
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Residues in contact with GLU 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ARG* 3.6 17.0 - - - +
599A ALA* 2.7 28.9 + - + -
600A CYS* 3.1 35.7 + - - -
579D ALA* 3.2 3.1 - - - +
580D SER* 2.9 45.0 + - - +
708D CYS* 1.3 78.3 - - - +
710D ALA* 1.3 65.1 + - - +
792D TYR* 2.9 27.2 + - + +
793D ILE 3.3 13.5 - - - +
794D SER* 4.4 0.9 - - - -
847D MET* 3.6 4.9 - - - -
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Residues in contact with ALA 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D ILE* 4.5 6.1 - - + +
578D GLY 3.9 17.9 - - - +
579D ALA* 4.0 4.7 - - + -
709D GLU* 1.3 80.2 - - - +
711D VAL* 1.3 66.3 + - - +
712D ILE* 4.2 16.2 - - + -
791D LEU 3.6 0.3 - - - +
792D TYR* 3.6 4.7 - - - -
793D ILE* 3.1 33.8 + - + +
847D MET* 3.7 17.0 - - + -
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Residues in contact with VAL 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ARG* 4.0 27.1 - - - +
576D GLY* 3.5 20.2 + - - +
578D GLY 4.9 2.6 + - - -
710D ALA* 1.3 79.1 - - - +
712D ILE* 1.3 66.3 + - - +
713D PRO* 3.5 11.1 - - + +
784D SER* 4.4 12.6 - - - +
785D GLY* 6.1 0.7 - - - -
790D ASP* 3.9 25.4 - - + -
791D LEU 3.2 9.6 - - - +
792D TYR* 4.1 16.8 - - + -
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Residues in contact with ILE 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ALA* 3.6 23.8 - - + +
573D ILE* 3.7 20.0 - - + -
710D ALA* 4.4 7.6 - - + -
711D VAL* 1.3 79.5 - - - +
713D PRO* 1.4 68.7 - - + +
716D VAL* 3.5 33.2 - - + -
717D VAL* 3.8 16.4 - - + +
721D LEU* 4.5 3.1 - - + -
790D ASP* 4.3 1.8 - - - -
791D LEU* 2.7 47.0 + - + +
793D ILE* 4.8 3.6 - - + -
851D LEU* 3.9 33.2 - - + -
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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