Contacts of the strand formed by residues 703 - 712 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585B ALA* 3.7 2.1 - - - +
586B ASP* 3.4 5.0 + - - -
587B GLY 2.7 46.6 + - - +
588B MET* 4.0 16.8 - - - +
648B GLN* 5.1 0.9 + - - -
702B ARG* 1.3 76.6 + - - +
704B LYS* 1.3 66.5 + - - -
705B SER* 3.9 1.6 + - - -
800B ILE 3.6 7.9 - - - -
801B GLU* 4.8 0.4 - - - -
802B ILE 5.7 0.2 - - - -
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Residues in contact with LYS 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B VAL* 4.6 7.6 - - + -
585B ALA 3.4 8.3 - - - +
586B ASP* 3.1 35.7 + - + -
651B SER* 5.0 3.2 + - - -
652B GLY 4.8 6.6 + - - -
654B ALA 4.8 5.5 + - - -
655B MET 5.6 1.6 + - - -
702B ARG 3.4 0.2 + - - -
703B GLY* 1.3 75.7 - - - -
705B SER* 1.3 62.3 + - - +
706B VAL* 3.9 4.2 + - + +
797B MET 3.6 3.6 - - - +
798B PRO 3.7 2.0 - - - +
800B ILE* 2.8 43.0 + - + +
802B ILE* 3.9 33.6 + - + +
832B GLY 4.8 0.4 - - - -
835B ALA* 3.9 23.0 - - - +
836B ARG* 4.1 14.4 - - + +
839B ALA* 3.8 26.0 - - + -
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Residues in contact with SER 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B VAL* 3.6 2.6 - - - +
584B LEU* 2.7 38.8 + - - -
585B ALA* 3.0 32.5 + - - +
700B GLU 5.1 0.2 + - - -
701B GLY* 4.0 9.7 - - - -
702B ARG 4.6 0.7 + - - -
703B GLY 3.9 1.4 + - - -
704B LYS* 1.3 71.6 - - - +
706B VAL* 1.3 63.0 + - - +
797B MET 3.4 5.4 - - - -
798B PRO* 2.6 29.1 + - - +
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Residues in contact with VAL 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B SER* 4.7 1.1 - - - -
582B ARG 3.3 17.3 - - - +
583B VAL* 4.3 6.3 - - + -
584B LEU* 4.1 4.9 - - - +
704B LYS* 4.1 7.9 - - + +
705B SER* 1.3 77.9 - - - +
707B VAL* 1.3 69.4 + - - +
796B THR* 3.5 4.0 - - - +
797B MET 2.8 38.1 + - - -
800B ILE* 3.7 25.4 - - + -
839B ALA* 4.1 19.1 - - + +
840B ARG* 4.4 12.8 - - + -
843B CYS* 3.4 29.1 - - + -
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Residues in contact with VAL 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B SER* 3.1 5.2 - - - -
582B ARG* 3.0 45.6 + - + +
584B LEU* 4.1 20.2 - - + +
706B VAL* 1.3 79.0 - - - +
708B CYS* 1.3 66.5 + - - +
795B CYS 3.4 5.4 - - - +
796B THR* 3.5 22.9 - - - +
599C ALA* 3.7 35.2 - - + +
638C ILE* 4.1 6.1 - - + -
640C GLY* 3.8 11.0 - - - +
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Residues in contact with CYS 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B LEU* 3.9 17.9 - - - -
579B ALA* 4.1 1.3 - - - -
580B SER 3.4 13.0 - - - -
581B SER* 3.9 6.1 - - - -
707B VAL* 1.3 75.9 - - - +
709B GLU* 1.3 70.5 + - - +
794B SER* 3.1 7.4 - - - -
795B CYS 2.9 28.9 + - - +
843B CYS* 3.8 21.5 - - - +
844B GLY* 3.6 20.0 - - - -
847B MET* 3.6 27.1 - - + -
599C ALA* 5.2 0.4 - - - -
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Residues in contact with GLU 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B ALA* 3.2 5.4 - - - +
580B SER* 3.0 45.6 + - - +
708B CYS* 1.3 78.8 - - - +
710B ALA* 1.3 62.5 + - - +
792B TYR* 2.8 33.7 + - + +
793B ILE 3.1 13.5 - - - +
794B SER* 4.3 0.9 - - - -
847B MET* 3.6 4.5 - - - -
598C ARG* 3.5 15.0 - - - +
599C ALA* 2.7 30.5 + - + -
600C CYS* 3.1 34.7 + - - -
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Residues in contact with ALA 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B ILE* 4.5 6.5 - - + +
578B GLY 4.0 17.3 - - - +
579B ALA* 4.0 3.8 - - + -
709B GLU* 1.3 77.9 - - - +
711B VAL* 1.3 64.8 + - - +
712B ILE* 4.1 17.9 - - + -
792B TYR* 3.6 5.0 - - - -
793B ILE* 3.0 35.5 + - + +
847B MET* 3.7 16.6 - - + -
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Residues in contact with VAL 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B GLY* 3.4 23.1 + - - +
578B GLY 4.8 2.4 + - - -
710B ALA* 1.3 78.1 - - - +
712B ILE* 1.3 69.7 + - - +
713B PRO* 3.5 8.1 - - + +
784B SER* 4.6 14.1 - - - +
790B ASP* 4.1 24.0 - - + +
791B LEU 3.2 7.9 - - - +
792B TYR* 4.1 20.2 - - + -
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Residues in contact with ILE 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ALA* 3.7 25.1 - - + +
573B ILE* 3.9 14.4 - - + +
710B ALA* 4.2 9.9 - - + -
711B VAL* 1.3 81.6 - - - +
713B PRO* 1.3 68.4 - - - +
716B VAL* 3.7 28.5 - - + -
717B VAL* 3.6 23.1 - - + +
721B LEU* 4.7 3.4 - - + -
791B LEU* 2.7 44.1 + - + +
793B ILE* 4.7 4.0 - - + -
851B LEU* 3.8 36.3 - - + -
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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