Contacts of the helix formed by residues 647 - 660 (chain A) in PDB entry 2PTM
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 PHE 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550A ASP* 4.3 16.6 - - + -
552A ASN* 3.6 23.6 - - + -
553A PHE* 3.4 59.5 - + + -
556A ARG* 4.4 6.7 - - + -
643A VAL* 2.9 21.7 + - + +
644A LEU 3.3 7.4 - - - +
646A GLU* 1.3 115.6 - - + +
648A PRO* 1.3 66.4 - - - +
649A ALA* 3.2 3.1 - - + -
650A MET* 3.0 25.3 + - + +
651A ARG 3.7 1.0 + - - -
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Residues in contact with PRO 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 3.3 12.3 - - - +
645A ASP* 3.7 12.6 - - - +
646A GLU 3.6 7.2 - - - +
647A PHE* 1.3 86.2 - - - +
649A ALA* 1.3 63.7 + - + +
651A ARG* 2.9 18.2 + - + +
652A LYS* 3.2 10.6 + - - +
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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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647A PHE* 3.1 1.7 + - + -
648A PRO* 1.3 80.5 - - + +
650A MET* 1.3 69.2 + - + +
652A LYS* 3.3 10.1 + - - +
653A THR* 3.1 31.8 + - + +
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Residues in contact with MET 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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545A PHE* 3.6 21.2 - - + +
549A ALA* 4.5 11.7 - - - -
550A ASP* 4.3 16.8 - - + +
553A PHE* 3.3 66.9 - - + -
644A LEU* 4.6 5.6 - - + -
647A PHE* 3.0 19.6 + - + +
649A ALA* 1.3 87.7 - - + +
651A ARG* 1.3 59.1 + - - +
652A LYS 3.2 0.9 - - - -
653A THR* 3.3 14.6 + - - -
654A MET* 3.0 29.1 + - - +
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Residues in contact with ARG 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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615A LEU* 3.9 17.4 + - - +
617A ARG* 4.3 18.1 - - - +
640A PHE* 4.8 1.0 - - - -
641A ASN* 3.3 25.1 + - - +
644A LEU* 3.4 59.9 + - + +
645A ASP* 3.9 15.5 + - - -
647A PHE 3.7 1.8 + - - -
648A PRO* 2.9 14.4 + - + +
650A MET* 1.3 77.3 - - - +
652A LYS* 1.3 59.5 + - - +
654A MET* 3.2 1.8 + - - +
655A GLU* 2.8 54.3 + - + +
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Residues in contact with LYS 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 PRO 3.2 7.1 + - - +
649A ALA* 3.4 13.2 - - - +
650A MET 3.2 0.4 - - - -
651A ARG* 1.3 80.6 - - - +
653A THR* 1.3 64.3 + - + +
655A GLU* 3.3 11.7 + - - +
656A GLU* 3.1 36.5 + - - +
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Residues in contact with THR 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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545A PHE* 3.1 26.6 + - - -
649A ALA* 3.1 19.9 + - + +
650A MET* 3.3 14.6 + - - +
652A LYS* 1.3 76.0 - - + +
654A MET* 1.3 62.6 + - - +
656A GLU* 3.4 17.6 + - - +
657A ILE* 2.9 31.2 - - - +
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Residues in contact with MET 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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545A PHE* 3.7 30.1 - - + -
553A PHE* 5.8 0.4 - - + -
582A MET* 4.6 9.0 - - + +
584A PHE* 5.7 2.2 - - + -
608A TYR* 4.0 25.8 - - - -
611A GLU* 4.1 22.6 - - + +
615A LEU* 3.9 25.1 - - + -
635A LEU* 6.5 0.2 - - + -
640A PHE* 3.8 20.2 - - + -
644A LEU* 4.3 13.5 - - + -
650A MET 3.0 15.4 + - - +
651A ARG* 3.6 6.1 - - - +
653A THR* 1.3 76.2 + - - +
655A GLU* 1.3 66.2 + - - +
656A GLU 3.2 0.5 + - - -
657A ILE* 3.3 5.0 + - - +
658A ALA* 3.2 19.1 + - - +
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Residues in contact with GLU 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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615A LEU* 4.2 19.9 - - + +
651A ARG* 2.8 49.0 + - - +
652A LYS* 3.8 10.8 - - - +
654A MET* 1.3 73.6 - - - +
656A GLU* 1.3 60.7 + - + +
658A ALA* 3.2 8.4 + - - +
659A VAL* 2.8 34.0 + - + +
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Residues in contact with GLU 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 LYS* 3.1 27.3 + - - +
653A THR* 3.7 16.4 - - - +
654A MET 3.1 0.6 - - - -
655A GLU* 1.3 78.2 - - + +
657A ILE* 1.3 61.4 + - + +
659A VAL* 3.6 7.3 + - - +
660A ARG* 3.1 35.8 + - + +
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Residues in contact with ILE 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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545A PHE* 5.7 3.8 - - + -
608A TYR* 3.6 29.6 - - + +
611A GLU* 4.5 0.9 - - - +
653A THR* 2.9 30.3 - - - +
654A MET 3.3 3.5 + - - +
656A GLU* 1.3 78.3 - - + +
658A ALA* 1.3 66.8 + - - +
660A ARG* 3.1 10.6 + - + +
661A ARG* 3.0 50.6 + - + +
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Residues in contact with ALA 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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611A GLU* 4.2 3.9 + - - +
612A ILE* 3.2 35.9 - - + +
615A LEU* 3.5 26.2 - - + -
654A MET 3.2 5.9 + - - +
655A GLU* 3.2 10.1 + - - +
657A ILE* 1.3 76.5 - - - +
659A VAL* 1.3 62.9 + - + +
661A ARG* 3.3 18.6 + - - +
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Residues in contact with VAL 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 GLU* 2.8 24.2 - - + +
656A GLU* 3.9 7.2 - - - +
658A ALA* 1.3 77.1 - - + +
660A ARG* 1.3 58.3 + - + +
661A ARG 2.8 14.0 + - - +
662A LEU* 3.6 13.1 - - - +
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Residues in contact with ARG 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 GLU* 3.1 24.4 + - - +
657A ILE* 3.1 15.4 + - + +
659A VAL* 1.3 73.3 - - + +
661A ARG* 1.3 61.4 + - - +
662A LEU* 3.5 20.0 + - + +
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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