Contacts of the helix formed by residues 729 - 743 (chain A) in PDB entry 1PD0
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 PRO 729 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A ILE* 4.7 6.7 - - + +
728A VAL* 1.3 91.7 - - + +
730A SER* 1.3 66.6 + - - +
731A ASP 3.4 0.9 - - - +
732A HIS* 3.2 28.5 + - + +
733A ARG* 3.1 17.8 + - - +
234B THR* 4.7 9.9 - - + +
235B TYR 5.6 5.8 - - - +
236B ASN* 5.1 3.4 - - - +
240B PRO* 3.6 27.4 - - + +
242B MET 5.9 2.0 - - - +
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Residues in contact with SER 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR* 4.4 17.5 + - - -
510A ALA* 5.2 8.7 - - - +
728A VAL 3.3 3.2 + - - -
729A PRO* 1.3 71.2 - - - +
731A ASP* 1.3 64.9 + - - +
733A ARG* 3.3 5.7 + - - +
734A ALA* 3.1 22.9 + - - +
234B THR* 3.9 14.8 + - - -
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Residues in contact with ASP 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR* 3.6 9.9 - - - -
507A MET* 2.8 25.8 + - - +
508A ASP* 2.9 25.8 + - - -
509A VAL* 2.9 24.3 + - + +
510A ALA 4.7 0.3 + - - -
525A PHE* 3.4 21.3 - - + -
729A PRO* 3.4 0.6 - - - +
730A SER* 1.3 79.0 + - - +
732A HIS* 1.3 65.2 + - - +
734A ALA* 3.4 1.7 + - - +
735A SER* 2.9 25.1 + - - -
234B THR* 3.4 7.2 + - + +
236B ASN* 3.2 21.7 + - - +
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Residues in contact with HIS 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A PHE* 4.0 3.1 - + - -
527A PRO* 3.7 19.4 - - + +
721A MET* 4.0 21.5 - - - +
728A VAL* 4.0 7.4 - - + -
729A PRO* 3.2 26.9 + - + +
731A ASP* 1.3 76.3 - - - +
733A ARG* 1.3 58.0 + - - +
735A SER* 3.1 8.3 + - - -
736A ALA* 2.8 30.3 + - - +
235B TYR 5.5 0.7 - - - -
236B ASN* 3.8 18.9 + - - -
237B ASN 2.8 33.0 + - - -
238B SER 3.8 8.1 + - - -
239B ASN 4.7 0.4 - - - -
240B PRO* 3.7 29.5 - - + +
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Residues in contact with ARG 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU* 3.5 34.4 - - - +
721A MET 3.4 21.0 + - - -
722A ALA* 3.5 12.7 + - - +
723A PHE 3.5 1.4 - - - -
724A ARG* 2.6 50.5 + - - +
725A SER 5.1 0.2 - - - -
726A GLY 4.2 10.7 + - - -
728A VAL* 3.6 39.2 + - + +
729A PRO 3.1 10.1 + - - +
730A SER* 3.5 11.0 - - - +
732A HIS* 1.3 78.2 - - - +
734A ALA* 1.3 65.0 + - - +
736A ALA* 3.0 5.3 + - - +
737A LEU* 2.9 32.1 + - + +
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Residues in contact with ALA 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A VAL* 3.9 7.2 - - + +
510A ALA* 3.4 42.8 - - + +
513A SER* 5.5 1.8 + - - +
517A ARG* 5.2 1.6 + - - -
664A LEU* 6.1 2.9 - - + -
730A SER 3.1 13.7 + - - +
731A ASP 3.8 3.6 - - - +
733A ARG* 1.3 78.9 - - - +
735A SER* 1.3 52.9 + - - +
737A LEU* 3.2 12.2 + - - +
738A ASN* 2.8 35.3 + - - +
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Residues in contact with SER 735 (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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509A VAL* 4.1 9.1 - - - +
525A PHE* 3.5 37.2 + - - +
731A ASP 2.9 14.0 + - - -
732A HIS* 3.2 9.9 - - - -
734A ALA* 1.3 77.1 - - - +
736A ALA* 1.3 62.6 + - - +
738A ASN* 3.1 8.0 + - - +
739A ASN* 2.9 25.3 + - - +
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Residues in contact with ALA 736 (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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720A HIS* 3.9 12.3 - - + -
721A MET* 4.1 13.9 - - + -
722A ALA* 3.7 27.8 - - + +
732A HIS 2.8 15.2 + - - +
733A ARG 3.5 7.6 - - - +
735A SER* 1.3 72.4 - - - +
737A LEU* 1.3 58.7 + - - +
739A ASN* 3.3 6.5 + - - +
740A LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 737 (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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517A ARG* 5.4 1.1 - - - +
660A VAL* 4.2 20.5 - - + +
663A ALA* 4.3 15.7 - - + -
664A LEU* 4.0 27.1 - - + +
668A LEU* 4.9 3.6 - - + -
722A ALA* 3.7 31.4 - - + +
723A PHE* 3.9 23.1 - - + -
733A ARG* 2.9 28.6 + - + +
734A ALA* 3.5 12.3 - - - +
736A ALA* 1.3 75.8 - - - +
738A ASN* 1.3 63.4 + - - +
740A LEU* 3.5 3.0 + - - +
741A GLU* 3.1 26.2 + - - +
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Residues in contact with ASN 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A VAL* 5.5 1.5 - - + +
513A SER* 4.5 13.9 - - - +
516A SER* 4.8 0.5 + - - -
517A ARG* 3.5 24.2 + - - +
522A GLN* 2.8 23.6 + - - -
523A THR* 3.3 23.8 + - - +
574A HIS* 3.0 27.2 + - - -
734A ALA 2.8 17.8 + - - +
735A SER* 3.1 8.5 + - - +
737A LEU* 1.3 76.3 - - - +
739A ASN* 1.3 62.4 + - - +
741A GLU* 3.3 11.5 - - - +
742A SER* 3.0 19.4 + - - -
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Residues in contact with ASN 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A GLN* 5.2 5.4 + - - +
720A HIS* 6.3 0.2 - - - -
735A SER* 2.9 16.1 + - - +
736A ALA* 3.7 6.5 - - - +
738A ASN* 1.3 75.4 - - - +
740A LEU* 1.3 66.0 + - - +
741A GLU 3.1 1.3 + - - -
742A SER* 3.1 5.5 + - - -
743A LEU* 3.0 67.1 + - - +
751A ASN* 3.4 17.4 + - - +
806A ASN* 3.5 13.7 + - - -
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Residues in contact with LEU 740 (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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656A ASN* 3.0 31.9 + - - +
660A VAL* 4.6 4.0 - - + -
717A LEU* 3.9 8.7 - - + -
720A HIS* 3.6 30.7 - - + +
722A ALA* 3.7 14.6 - - + -
723A PHE* 3.6 30.7 - - + -
736A ALA 2.9 17.8 + - - +
737A LEU 4.0 3.4 - - - +
739A ASN* 1.3 76.1 - - - +
741A GLU* 1.3 60.8 + - - +
742A SER 3.5 0.5 + - - -
743A LEU* 4.1 8.2 + - + +
748A LEU* 3.7 29.4 - - + +
751A ASN* 4.2 15.7 - - + +
752A ILE* 4.5 3.1 - - + -
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Residues in contact with GLU 741 (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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517A ARG* 2.6 41.3 + - - +
572A TYR* 5.5 0.7 - - - +
573A GLY* 4.3 20.3 + - - +
574A HIS* 2.9 24.8 + - + +
593A SER 4.6 2.4 - - - +
656A ASN* 4.5 5.2 - - - +
657A SER* 4.8 11.5 + - - +
660A VAL* 3.9 29.0 - - + +
664A LEU* 4.5 2.9 - - - +
737A LEU 3.1 12.5 + - - +
738A ASN* 3.3 14.7 - - - +
739A ASN 3.1 1.4 + - - -
740A LEU* 1.3 80.4 - - - +
742A SER* 1.3 57.9 + - - +
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Residues in contact with SER 742 (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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522A GLN* 3.0 25.5 + - - -
573A GLY* 5.6 0.2 - - - -
574A HIS* 3.9 13.9 - - - -
591A ASP 4.2 0.3 - - - +
592A GLN* 3.3 32.2 - - - +
593A SER* 2.9 33.6 + - - -
738A ASN 3.0 13.0 + - - -
739A ASN* 3.1 3.3 + - - -
741A GLU* 1.3 77.3 - - - +
743A LEU* 1.3 65.0 + - - +
744A PRO* 3.9 0.2 - - - +
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Residues in contact with LEU 743 (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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591A ASP 5.7 0.2 - - - +
593A SER* 3.3 9.6 - - - -
739A ASN* 3.0 55.4 + - - +
740A LEU* 4.1 8.3 + - + +
741A GLU 3.8 0.6 - - - -
742A SER* 1.3 80.1 + - - +
744A PRO* 1.3 78.2 - - + +
745A LEU 3.5 1.0 + - - -
747A TYR* 3.9 29.6 - - + +
748A LEU* 4.2 18.9 - - + +
751A ASN* 3.5 24.0 - - + +
865A VAL* 5.6 4.0 - - + -
867A THR* 5.8 3.8 - - - +
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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