Contacts of the helix formed by residues 647 - 666 (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 ASP 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PRO* 3.4 17.4 - - + +
159A PRO* 4.1 7.2 - - + -
183A ARG* 2.7 52.2 + - - +
184A SER 3.3 20.8 - - - +
185A THR 2.9 9.2 + - - +
187A ASN* 4.7 3.7 + - - +
645A SER 3.5 1.0 + - - -
646A ALA* 1.3 68.7 - - - +
648A GLN* 1.3 64.4 + - - +
649A LEU* 3.2 4.5 + - - +
650A ALA* 3.1 19.3 + - + +
651A ILE* 2.9 25.1 + - - +
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Residues in contact with GLN 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 4.4 17.6 + - - +
156A LEU* 6.1 0.6 - - - +
159A PRO* 5.5 0.4 - - - +
646A ALA 3.4 6.3 + - - -
647A ASP* 1.3 72.6 + - - +
649A LEU* 1.3 74.7 + - + +
651A ILE* 3.3 5.3 + - - +
652A ALA* 2.8 30.0 + - - +
705A ALA 4.7 2.2 + - - -
706A ASN* 2.9 29.7 + - - +
707A LEU* 3.3 20.1 - - + -
708A ARG 3.4 0.3 + - - -
709A MET* 2.8 49.3 + - + +
710A PHE* 4.2 12.9 - - + +
713A LEU* 4.8 1.3 - - + +
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Residues in contact with LEU 649 (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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153A ASP 5.1 1.3 - - - +
154A LEU* 3.6 33.2 - - + +
156A LEU 4.7 9.4 - - - +
183A ARG* 3.7 27.8 - - - +
647A ASP* 3.2 1.6 + - - -
648A GLN* 1.3 90.9 - - + +
650A ALA* 1.3 63.1 + - - +
652A ALA* 3.4 5.2 + - - +
653A SER 3.1 16.6 + - - -
713A LEU* 3.6 18.4 - - + -
745A LEU* 3.4 22.3 - - + +
749A ILE* 3.6 37.5 - - + +
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Residues in contact with ALA 650 (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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183A ARG* 4.1 5.3 - - + +
184A SER 4.1 2.5 - - - +
185A THR* 3.8 20.3 - - + +
206A VAL* 3.8 27.5 - - + +
595A LEU* 4.7 0.3 - - - +
647A ASP* 3.0 34.3 + - + +
649A LEU* 1.3 73.2 - - - +
651A ILE* 1.3 61.3 + - - +
653A SER* 3.2 5.3 + - - -
654A PHE* 2.8 26.7 + - - +
745A LEU* 4.8 1.8 - - - -
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Residues in contact with ILE 651 (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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185A THR* 3.7 31.4 - - + +
201A LEU* 4.1 19.1 - - + -
202A PRO* 4.0 10.5 - - + -
646A ALA* 3.9 20.2 - - + -
647A ASP 2.9 19.1 + - - +
648A GLN* 3.6 7.4 - - - +
650A ALA* 1.3 74.9 - - - +
652A ALA* 1.3 65.3 + - - +
654A PHE* 2.9 18.1 + - - +
655A TYR* 3.0 31.8 + - + -
682A ILE* 4.8 2.9 - - + -
707A LEU* 4.1 8.1 - - + -
710A PHE* 3.4 25.8 - - + -
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Residues in contact with ALA 652 (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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648A GLN 2.8 17.6 + - - +
649A LEU* 3.5 6.7 - - - +
650A ALA 3.3 0.2 - - - -
651A ILE* 1.3 75.3 - - - +
653A SER* 1.3 57.5 + - - +
655A TYR 3.5 0.5 + - - -
656A ASN* 2.9 29.3 + - - +
710A PHE* 3.9 7.2 - - + -
713A LEU* 3.9 24.2 - - + -
714A MET* 3.7 30.4 - - + +
748A LEU* 5.5 0.2 - - - -
749A ILE* 4.4 7.2 - - + -
752A ILE* 5.5 4.0 - - + +
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Residues in contact with SER 653 (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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206A VAL* 4.3 12.3 - - - +
595A LEU* 3.8 10.7 - - - +
649A LEU 3.1 13.5 + - - -
650A ALA* 3.2 11.4 - - - -
651A ILE 3.1 0.2 - - - -
652A ALA* 1.3 76.0 - - - +
654A PHE* 1.3 64.9 + - - +
656A ASN* 3.1 9.2 + - - +
657A SER* 3.0 25.1 + - - -
745A LEU* 3.9 17.3 - - - +
748A LEU* 3.7 16.4 - - - +
749A ILE* 5.5 0.4 - - - +
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Residues in contact with PHE 654 (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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185A THR* 4.3 3.4 - - + -
202A PRO* 3.3 37.0 - - + -
203A PHE 4.0 9.9 - - - -
204A GLY* 4.0 12.3 - - - -
595A LEU* 3.6 27.2 - - + +
597A GLU* 3.4 44.4 - - + -
650A ALA 2.8 12.8 + - - +
651A ILE* 2.9 14.9 + - - +
653A SER* 1.3 75.2 - - - +
655A TYR* 1.3 74.9 + + - +
657A SER* 3.1 7.1 + - - -
658A LYS* 3.0 49.9 + - + +
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Residues in contact with TYR 655 (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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200A LYS 3.7 12.8 + - - -
202A PRO* 3.5 29.4 - - + +
651A ILE* 3.0 34.4 + - + +
654A PHE* 1.3 91.6 - + - +
656A ASN* 1.3 59.9 + - - +
657A SER 3.2 0.2 - - - -
658A LYS* 3.8 6.1 - - + +
659A ALA* 2.8 31.2 + - - +
674A LEU* 4.1 20.5 - - + +
675A ILE* 5.0 1.9 - - - +
678A SER* 3.6 35.3 + - - +
682A ILE* 4.7 3.9 - - + +
710A PHE* 3.7 15.3 - + - -
714A MET* 3.9 18.4 - - - -
717A LEU* 4.8 2.9 - - - +
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Residues in contact with ASN 656 (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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652A ALA 2.9 19.2 + - - +
653A SER* 3.3 11.5 + - - +
654A PHE 3.1 0.4 - - - -
655A TYR* 1.3 79.6 - - - +
657A SER* 1.3 64.4 + - - +
659A ALA* 3.4 3.1 + - - +
660A VAL* 3.1 27.1 + - - +
717A LEU* 4.0 22.7 - - + +
723A PHE* 4.5 1.6 - - - -
740A LEU* 3.0 54.6 + - - +
741A GLU* 4.5 2.0 - - - +
748A LEU* 3.6 22.9 - - + +
752A ILE* 5.0 2.7 - - + -
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Residues in contact with SER 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A TYR* 4.0 39.2 - - - +
595A LEU* 4.4 13.8 - - - +
653A SER* 3.0 13.8 + - - -
654A PHE 3.6 7.0 - - - -
656A ASN* 1.3 81.3 + - - +
658A LYS* 1.3 64.6 + - - +
660A VAL* 3.1 7.5 + - - +
661A GLU* 2.9 23.4 + - - +
741A GLU* 4.8 11.6 + - - +
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Residues in contact with LYS 658 (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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570A ARG* 4.2 8.1 - - - +
572A TYR* 3.1 30.5 + - + +
597A GLU* 2.7 29.5 + - - -
654A PHE* 3.0 56.0 + - + +
655A TYR* 3.9 8.5 - - + +
657A SER* 1.3 75.2 - - - +
659A ALA* 1.3 58.2 + - - +
661A GLU* 3.3 12.6 + - - +
662A LYS* 2.8 30.1 + - - +
674A LEU* 4.1 24.5 - - + +
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Residues in contact with ALA 659 (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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655A TYR 2.8 19.7 + - - +
656A ASN* 3.5 4.7 - - - +
658A LYS* 1.3 78.5 - - - +
660A VAL* 1.3 56.9 + - - +
662A LYS* 3.3 7.3 + - - +
663A ALA* 2.9 24.9 + - - +
671A ALA* 3.5 4.6 - - - +
674A LEU* 4.3 5.3 - - + +
675A ILE* 3.9 24.7 - - + -
723A PHE* 3.4 32.1 - - + -
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Residues in contact with VAL 660 (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* 3.1 21.4 + - - +
657A SER* 3.1 8.5 + - - +
659A ALA* 1.3 75.9 - - - +
661A GLU* 1.3 58.6 + - - +
663A ALA* 3.8 0.2 - - - +
664A LEU* 2.8 53.1 + - + +
723A PHE* 3.8 17.7 - - + -
737A LEU* 4.2 21.8 - - + +
740A LEU* 4.6 2.9 - - + -
741A GLU* 3.9 40.4 - - + +
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Residues in contact with GLU 661 (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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570A ARG* 2.6 35.6 + - - -
572A TYR* 2.8 31.4 + - + -
657A SER 2.9 13.0 + - - +
658A LYS* 3.4 16.8 + - - +
660A VAL* 1.3 75.3 - - - +
662A LYS* 1.3 68.7 + - - +
664A LEU* 3.7 4.7 - - - +
665A ASN* 2.9 45.9 + - + +
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Residues in contact with LYS 662 (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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658A LYS 2.8 17.4 + - - +
659A ALA* 3.5 6.5 - - - +
661A GLU* 1.3 77.7 - - - +
663A ALA* 1.3 54.4 + - - +
665A ASN* 4.0 5.8 + - - +
666A SER* 2.6 46.9 + - - -
667A SER 3.2 1.9 + - - -
670A ASP* 3.8 29.8 - - + +
671A ALA* 3.8 26.2 - - - +
674A LEU* 4.1 21.2 - - + +
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Residues in contact with ALA 663 (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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659A ALA 2.9 17.1 + - - +
660A VAL 3.8 2.7 - - - +
662A LYS* 1.3 77.9 - - - +
664A LEU* 1.3 56.3 + - - +
665A ASN 2.7 13.0 + - - -
666A SER 3.2 12.3 + - - +
667A SER* 3.6 14.3 + - - -
668A LEU* 3.8 26.7 - - + -
671A ALA* 3.9 7.7 - - + +
723A PHE* 4.1 9.6 - - + -
737A LEU* 4.3 11.0 - - + -
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Residues in contact with LEU 664 (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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510A ALA* 6.1 5.8 - - + +
517A ARG* 4.2 37.9 - - - +
660A VAL* 2.8 43.5 + - + +
661A GLU* 4.0 3.6 - - - +
663A ALA* 1.3 71.7 - - - +
665A ASN* 1.3 58.2 + - + +
734A ALA* 6.1 2.2 - - + -
737A LEU* 4.0 24.7 - - + +
741A GLU* 4.5 3.1 - - - +
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Residues in contact with ASN 665 (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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661A GLU* 2.9 37.0 + - + +
662A LYS* 3.4 7.8 + - - +
663A ALA 2.7 6.0 + - - -
664A LEU* 1.3 77.1 - - + +
666A SER* 1.3 74.5 + - - +
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Residues in contact with SER 666 (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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662A LYS* 2.6 27.9 + - - -
663A ALA 3.7 3.9 - - - +
665A ASN* 1.3 85.4 + - - +
667A SER* 1.3 70.7 + - - -
670A ASP* 3.4 27.2 + - - -
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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
------------------------------------------------------------
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