Contacts of the strand formed by residues 703 - 712 (chain C) in PDB entry 1DQA
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585C ALA* 3.8 1.6 - - - +
586C ASP* 3.3 5.5 + - - -
587C GLY 2.8 44.7 + - - +
588C MET* 4.1 17.4 - - - +
648C GLN* 5.1 1.0 + - - -
702C ARG* 1.3 77.2 + - - +
704C LYS* 1.3 65.7 + - - -
705C SER* 4.1 1.2 + - - -
800C ILE 3.6 7.0 - - - -
801C GLU* 4.7 0.9 - - - -
802C ILE 5.6 0.2 - - - -
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Residues in contact with LYS 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C VAL* 4.8 3.4 - - + -
585C ALA 3.4 5.6 - - - +
586C ASP* 2.7 45.6 + - + +
651C SER* 5.0 3.0 + - - -
652C GLY 4.8 5.8 + - - -
654C ALA 4.9 4.9 + - - -
655C MET 5.9 0.6 + - - -
702C ARG 3.3 0.4 + - - -
703C GLY* 1.3 74.4 - - - -
705C SER* 1.3 60.6 + - - +
706C VAL* 4.0 5.5 + - + -
797C MET 3.6 3.1 - - - +
798C PRO 3.7 1.9 - - - +
800C ILE* 2.8 45.8 + - - +
802C ILE* 4.1 18.0 + - + +
832C GLY 4.7 0.7 - - - -
835C ALA* 3.7 32.5 - - - +
836C ARG* 3.8 17.9 - - + +
839C ALA* 3.8 31.6 - - + -
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Residues in contact with SER 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C VAL* 3.5 1.7 - - - -
584C LEU* 2.6 46.7 + - - -
585C ALA* 3.0 30.1 + - - +
700C GLU 5.2 0.2 + - - -
701C GLY* 4.0 9.7 - - - -
702C ARG 4.7 0.5 + - - -
703C GLY 4.1 0.9 + - - -
704C LYS* 1.3 68.8 - - - +
706C VAL* 1.3 60.8 + - - +
797C MET 3.3 5.8 - - - -
798C PRO* 2.7 28.8 + - - +
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Residues in contact with VAL 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C SER* 4.6 2.0 - - - -
582C ARG 3.4 14.6 - - - +
583C VAL* 4.5 8.7 - - + -
584C LEU* 4.2 4.2 - - - +
704C LYS* 4.2 8.3 - - + -
705C SER* 1.3 81.6 - - - +
707C VAL* 1.3 70.0 + - - +
796C THR* 3.6 4.5 - - - +
797C MET 2.8 34.2 + - - +
800C ILE* 4.0 18.8 - - + -
839C ALA* 4.0 19.7 - - + -
840C ARG* 4.1 16.4 - - + -
843C CYS* 3.5 29.3 - - + -
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Residues in contact with VAL 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B ALA* 3.7 35.9 - - + +
638B ILE* 4.2 6.3 - - + -
640B GLY* 3.8 11.0 - - - +
581C SER* 3.1 5.8 - - - -
582C ARG* 2.9 49.3 + - + +
584C LEU* 4.0 24.9 - - + -
706C VAL* 1.3 76.7 - - - +
708C CYS* 1.3 66.1 + - - +
795C CYS 3.3 7.4 - - - +
796C THR* 3.5 21.8 - - - +
843C CYS* 4.1 2.7 - - - -
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Residues in contact with CYS 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B ALA* 5.2 0.7 - - - -
546C LEU* 4.9 2.9 - - + -
580C SER 3.1 12.8 - - - +
581C SER* 3.7 12.6 - - - +
707C VAL* 1.3 78.1 - - - +
709C GLU* 1.3 63.4 + - - +
794C SER* 3.2 5.9 - - - -
795C CYS* 3.0 34.3 + - - +
843C CYS* 3.3 39.5 - - - -
844C GLY* 3.8 8.3 - - - +
847C MET* 3.6 25.5 - - + +
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Residues in contact with GLU 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B ARG* 3.5 18.9 - - - +
599B ALA* 2.8 20.5 + - + -
600B CYS* 3.0 36.6 + - - -
579C ALA* 3.2 6.9 - - - +
580C SER* 2.9 42.7 + - - +
708C CYS* 1.3 78.8 - - - +
710C ALA* 1.3 61.9 + - - +
792C TYR* 2.7 40.8 + - + +
793C ILE 3.2 13.5 - - - +
794C SER* 4.3 1.3 - - - -
847C MET* 3.5 6.0 - - - -
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Residues in contact with ALA 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C ILE* 4.5 7.2 - - + +
578C GLY 3.9 17.7 - - - +
579C ALA* 4.2 2.9 - - + -
709C GLU* 1.3 79.5 - - - +
711C VAL* 1.3 63.8 + - - +
712C ILE* 4.5 12.3 - - + -
792C TYR* 3.5 6.0 - - - -
793C ILE* 2.9 39.6 + - + +
847C MET* 3.7 16.6 - - + -
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Residues in contact with VAL 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B ARG* 3.8 25.1 - - - +
576C GLY* 3.4 25.6 + - - +
578C GLY 4.9 2.0 + - - -
710C ALA* 1.3 79.6 - - - +
712C ILE* 1.3 66.0 + - - +
713C PRO* 3.7 5.3 - - + +
784C SER* 4.3 14.4 - - - +
785C GLY* 5.7 0.9 - - - +
790C ASP* 3.9 26.5 - - + +
791C LEU 3.2 7.0 - - - +
792C TYR* 3.9 15.3 - - + -
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Residues in contact with ILE 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C ALA* 3.7 22.7 - - + +
573C ILE* 3.8 14.6 - - + -
710C ALA* 4.5 7.6 - - + -
711C VAL* 1.3 80.8 - - - +
713C PRO* 1.3 68.1 - - + +
716C VAL* 3.5 31.2 - - + -
717C VAL* 3.6 24.1 - - + +
721C LEU* 4.6 2.5 - - + -
790C ASP* 3.6 2.5 - - - -
791C LEU* 2.7 45.0 + - + +
793C ILE* 4.8 3.4 - - + -
851C 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