Contacts of the helix formed by residues 646 - 660 (chain A) in PDB entry 2P8Q
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 TYR 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A ASP* 3.1 51.5 + - - +
608A MET* 3.9 17.7 - - + -
609A ALA* 4.8 7.3 - - + +
612A LEU* 3.8 25.6 - - + -
639A LEU* 3.8 12.8 - - + -
642A GLU 4.8 2.7 - - - -
643A PHE* 2.8 40.2 + + + +
645A LYS* 1.3 114.1 - - + +
647A MET* 1.3 54.9 + - - +
648A GLU 3.3 2.7 - - - -
649A ALA* 3.0 10.0 + - + +
650A PHE* 2.7 35.6 + - + +
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Residues in contact with MET 647 (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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643A PHE* 3.7 24.3 + - + -
644A LEU* 3.3 21.0 + - + +
646A TYR* 1.3 76.0 - - - +
648A GLU* 1.3 59.2 + - - +
650A PHE* 4.4 7.4 - - - +
651A LYS* 2.7 42.4 + - + +
654A LEU* 4.9 9.2 - - + -
677A LEU* 4.0 20.4 - - + -
681A LEU* 3.6 31.6 - - + -
685A ILE* 5.1 3.4 - - + -
688A PHE* 3.7 49.6 - - + -
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Residues in contact with GLU 648 (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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644A LEU 4.6 1.4 + - - -
645A LYS 5.1 4.0 + - - +
646A TYR 3.3 0.8 - - - -
647A MET* 1.3 79.1 - - - +
649A ALA* 1.3 58.3 + - - +
651A LYS* 2.7 36.8 + - - +
652A PRO* 4.2 9.5 - - - +
688A PHE* 4.5 9.3 - - - -
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Residues in contact with ALA 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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612A LEU* 3.8 24.2 - - + +
645A LYS 5.5 1.1 + - - +
646A TYR* 3.0 10.5 + - + +
648A GLU* 1.3 81.1 - - - +
650A PHE* 1.3 59.9 + - - +
651A LYS 3.5 0.4 - - - -
652A PRO* 3.5 15.4 - - - +
653A PHE* 3.7 12.0 - - - -
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Residues in contact with PHE 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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608A MET* 5.5 3.1 - - - -
612A LEU* 3.9 14.3 - - + +
615A PHE* 4.3 13.9 - + - -
629A LEU* 4.2 10.5 - - + -
632A VAL* 4.0 24.5 - - + -
643A PHE* 4.1 24.2 - + + -
646A TYR* 2.7 22.9 + - + +
647A MET* 4.1 9.2 - - - +
649A ALA* 1.3 72.3 - - - +
651A LYS* 1.3 67.0 + - - +
652A PRO* 3.3 2.2 - - - -
653A PHE* 2.8 29.4 + - + +
654A LEU* 3.0 39.8 + - + -
673A LEU* 3.4 34.1 - - + -
677A LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 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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647A MET* 2.7 24.3 + - + +
648A GLU* 2.7 40.7 + - - +
650A PHE* 1.3 72.7 - - - +
652A PRO* 1.3 70.4 - - + +
654A LEU* 3.1 16.1 + - + +
655A GLY* 3.0 18.4 + - - -
687A PRO 6.1 0.2 - - - -
688A PHE* 4.4 21.1 - - + -
691A GLU* 3.1 39.5 + - - +
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Residues in contact with PRO 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 GLU 4.2 5.2 - - - +
649A ALA* 3.5 18.2 - - - +
650A PHE 3.4 2.2 - - - -
651A LYS* 1.3 99.1 - - + +
653A PHE* 1.3 69.2 + - + +
655A GLY* 3.1 3.8 + - - +
656A ILE* 2.9 29.2 + - - +
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Residues in contact with PHE 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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612A LEU* 4.2 13.7 - - + -
615A PHE* 3.3 67.5 - + + -
616A GLN* 3.5 16.8 - - + -
619A ALA* 4.2 12.1 - - + -
624A VAL* 4.1 9.1 - - + +
629A LEU* 4.6 6.4 - - - +
649A ALA 3.7 22.7 - - - -
650A PHE* 2.8 24.2 + - + +
652A PRO* 1.3 77.3 - - + +
654A LEU* 1.3 63.3 + - - +
656A ILE* 3.0 29.1 - - + +
657A GLY* 3.4 6.4 + - - -
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Residues in contact with LEU 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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629A LEU* 5.5 2.2 - - + -
647A MET* 4.9 9.9 - - + -
650A PHE* 3.0 33.6 + - + +
651A LYS* 3.1 15.0 - - + +
653A PHE* 1.3 76.9 - - - +
655A GLY* 1.3 63.2 + - - +
657A GLY* 3.2 3.3 + - - -
658A LEU* 3.0 36.4 + - + +
670A ALA* 4.1 12.7 - - + +
673A LEU* 4.9 5.4 - - + -
674A VAL* 4.0 20.0 - - + -
677A LEU* 3.8 25.1 - - + -
692A VAL* 4.4 16.6 - - + -
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Residues in contact with GLY 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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651A LYS 3.0 12.9 + - - -
652A PRO* 3.1 4.9 + - - -
654A LEU* 1.3 72.1 - - - +
656A ILE* 1.3 51.3 + - - +
657A GLY 2.9 4.5 - - - -
658A LEU* 2.7 9.1 + - - +
659A LYS* 2.7 44.2 + - - +
695A LEU* 4.1 21.1 - - - -
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Residues in contact with ILE 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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619A ALA 6.2 0.4 - - - +
623A GLY 3.7 19.5 - - - +
624A VAL* 3.2 18.5 - - + +
652A PRO 2.9 8.0 + - - +
653A PHE* 3.0 39.7 - - + +
655A GLY* 1.3 71.5 - - - +
657A GLY* 1.3 55.8 + - - +
659A LYS* 4.3 14.5 - - + +
660A ASN* 3.2 28.4 + - + +
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Residues in contact with GLY 657 (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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624A VAL* 4.7 3.8 - - - -
629A LEU* 4.7 5.4 - - - -
653A PHE 3.4 5.1 + - - -
654A LEU 3.2 6.6 + - - -
655A GLY 2.9 1.2 - - - -
656A ILE* 1.3 85.6 - - - +
658A LEU* 1.3 59.9 + - - +
660A ASN* 3.4 8.3 - - - +
666A VAL* 4.0 15.7 - - - -
667A CYS* 3.3 24.3 + - - -
670A ALA* 3.5 12.5 - - - +
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Residues in contact with LEU 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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654A LEU* 3.0 38.1 + - + +
655A GLY* 2.7 13.0 + - - +
657A GLY* 1.3 70.3 - - - +
659A LYS* 1.3 62.0 + - - +
660A ASN 4.2 0.3 - - - -
667A CYS* 3.6 20.3 - - - -
670A ALA* 4.0 13.9 - - + -
671A VAL* 4.2 13.9 - - + -
674A VAL* 4.2 15.7 - - + -
692A VAL* 4.3 17.3 - - + -
695A LEU* 4.0 33.4 - - + +
696A LEU* 3.9 26.7 - - + -
699A ASN* 4.2 8.7 + - - +
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Residues in contact with LYS 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 GLY* 2.7 26.5 + - - +
656A ILE* 4.1 13.5 - - + +
658A LEU* 1.3 71.4 - - - +
660A ASN* 1.3 54.8 + - - +
661A TYR* 2.8 29.8 + - - +
695A LEU* 4.2 30.6 - - + +
698A GLU* 5.3 9.4 - - - +
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Residues in contact with ASN 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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624A VAL 5.5 4.8 + - - +
656A ILE* 3.2 21.3 + - + +
657A GLY* 3.4 7.5 - - - +
658A LEU 3.3 0.4 - - - -
659A LYS* 1.3 74.4 - - - +
661A TYR* 1.3 57.8 + - - +
662A ALA* 4.6 2.6 - - - +
663A GLU* 3.0 55.0 + - - +
666A VAL* 3.9 13.2 - - + +
667A CYS* 3.1 21.1 - - - +
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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