Contacts of the strand formed by residues 549 - 556 (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 LYS 549 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544D LEU 4.1 0.7 - - - -
545D CYS* 3.2 6.6 - - - +
546D LEU 2.9 32.8 + - - +
547D ASP* 4.0 17.0 - - - +
548D GLU* 1.3 84.2 - - + +
550D GLU* 1.3 66.9 + - - +
551D PHE* 3.9 23.3 - - + -
837D GLN* 3.3 26.4 + - - +
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Residues in contact with GLU 550 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C LYS 5.4 3.3 - - - +
543D PRO* 3.7 26.2 - - + +
544D LEU 3.4 3.6 - - - -
545D CYS* 4.1 22.3 - - + -
549D LYS* 1.3 80.6 - - - +
551D PHE* 1.3 65.7 + - - +
552D GLN* 4.2 5.7 + - - +
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Residues in contact with PHE 551 (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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542D GLY* 4.0 0.9 - - - -
543D PRO* 3.4 4.9 - - - +
544D LEU* 2.8 53.0 + - + +
546D LEU* 3.9 34.3 - - + -
547D ASP* 6.2 0.2 - - + -
549D LYS* 3.9 26.2 - - + -
550D GLU* 1.3 78.3 - - - +
552D GLN* 1.3 63.7 + - - +
553D VAL* 3.7 7.0 + - + -
820D MET 5.6 0.7 - - - -
821D LEU* 3.8 33.4 - - + -
837D GLN* 3.6 31.2 - - + -
841D ILE* 3.7 28.9 - - + -
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Residues in contact with GLN 552 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499C LEU* 3.6 34.6 - - + +
502C LYS* 3.8 32.6 + - + +
503C LEU* 4.1 19.1 - - + -
540D VAL* 4.0 13.1 - - + +
541D ALA 3.9 1.3 - - - -
542D GLY* 3.9 14.2 - - - +
543D PRO* 3.4 33.1 - - - +
550D GLU* 4.2 5.8 + - - +
551D PHE* 1.3 75.0 + - - +
553D VAL* 1.3 60.3 + - - +
554D PRO* 3.6 5.7 - - - +
820D MET* 4.3 12.6 + - + +
821D LEU* 3.3 15.1 - - - +
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Residues in contact with VAL 553 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539D GLY 3.6 0.3 - - - +
540D VAL* 3.3 7.0 - - - -
541D ALA* 2.8 47.5 + - + +
544D LEU* 4.3 13.0 - - + -
551D PHE* 4.2 12.1 - - + +
552D GLN* 1.3 71.7 - - - +
554D PRO* 1.4 76.2 - - + +
555D MET* 3.7 6.3 - - + +
570D CYS* 5.5 1.1 - - - -
760D ILE* 3.8 31.4 - - + -
821D LEU* 4.2 1.1 - - + -
841D ILE* 4.2 16.6 - - + -
845D THR* 3.6 26.9 - - + +
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Residues in contact with PRO 554 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531C ILE* 5.2 0.4 - - + -
538D VAL* 4.3 4.3 - - + -
539D GLY 3.4 6.3 - - - +
540D VAL* 4.7 1.8 - - + -
552D GLN 3.6 5.2 - - - +
553D VAL* 1.4 93.1 - - + +
555D MET* 1.3 63.8 + - - +
760D ILE* 3.8 10.6 - - - +
763D ALA* 3.8 10.9 - - + +
764D CYS* 4.5 4.0 - - - -
817D CYS* 3.7 50.5 - - + +
820D MET* 3.8 21.5 - - + -
821D LEU* 4.0 15.5 - - + -
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Residues in contact with MET 555 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527C CYS* 4.4 0.2 - - - -
538D VAL* 3.3 3.3 - - - +
539D GLY* 2.8 38.6 + - - +
541D ALA* 3.5 24.0 - - + +
553D VAL* 3.7 13.5 - - + +
554D PRO* 1.3 80.8 - - - +
556D ALA* 1.3 60.3 + - - +
557D THR* 3.6 5.9 + - + +
562D LEU* 4.6 3.1 - - + -
563D VAL* 3.3 46.7 - - + +
566D THR* 3.8 26.2 - - - +
756D ILE* 5.1 7.2 - - - -
759D ALA* 3.8 23.3 - - + -
760D ILE* 4.5 2.9 - - + -
763D ALA* 4.2 0.9 - - - -
845D THR* 4.6 8.1 - - - -
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Residues in contact with ALA 556 (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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534C MET* 4.4 1.1 - - + -
536D ILE* 3.7 15.3 - - + +
537D PRO 3.1 7.6 - - - +
538D VAL* 4.1 10.5 - - + +
555D MET* 1.3 68.5 - - - +
557D THR* 1.3 63.9 + - - +
758D THR* 5.8 0.2 - - - +
759D ALA* 3.0 22.0 + - - -
762D ILE* 3.6 25.2 - - + +
763D ALA* 3.6 31.2 - - + +
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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