Contacts of the helix formed by residues 611 - 622 (chain T) in PDB entry 2P8Z
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 611 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609T ARG 3.7 0.2 + - - -
610T ASP* 1.3 72.1 - - - +
612T PHE* 1.3 78.0 + - - +
613T LYS* 3.0 20.0 + - - +
614T ALA* 2.9 35.5 + - + +
615T ARG* 3.0 20.4 + - - +
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Residues in contact with PHE 612 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610T ASP 3.1 4.8 + - - -
611T ASP* 1.3 79.6 - - - +
613T LYS* 1.3 70.1 + - + +
615T ARG* 3.8 29.3 + - - +
616T ALA* 3.0 30.1 + - - +
630T ALA 4.9 0.7 - - - +
631T ARG* 3.4 72.6 - - + +
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Residues in contact with LYS 613 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611T ASP* 3.0 15.7 + - - +
612T PHE* 1.3 96.1 - - + +
614T ALA* 1.3 70.2 + - - +
616T ALA* 3.1 7.0 + - - +
617T ARG* 3.0 29.0 + - + +
627T VAL* 5.7 0.2 - - - +
631T ARG* 4.9 16.8 - - - +
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Residues in contact with ALA 614 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610T ASP* 6.4 0.7 - - + -
611T ASP* 2.9 24.2 + - + +
613T LYS* 1.3 75.9 - - - +
615T ARG* 1.3 62.0 + - - +
617T ARG* 3.2 9.9 + - - +
618T ILE* 3.2 30.0 + - + +
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Residues in contact with ARG 615 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606T ILE* 3.9 21.1 - - + -
607T ASN 2.8 40.4 + - - +
608T PRO 3.2 18.2 + - - -
610T ASP* 3.8 17.7 + - + +
611T ASP 3.0 16.2 + - - +
612T PHE* 3.8 29.8 + - - +
614T ALA* 1.3 77.8 - - - +
616T ALA* 1.3 55.6 + - - +
618T ILE* 3.1 11.3 + - - +
619T MET* 2.9 55.5 + - + +
630T ALA 4.9 1.6 + - - -
631T ARG 5.7 0.2 + - - -
633T ILE* 3.6 25.6 + - - +
636T PHE* 3.6 16.6 - - - -
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Residues in contact with ALA 616 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612T PHE 3.0 19.9 + - - +
613T LYS 3.1 4.0 + - - +
615T ARG* 1.3 76.7 - - - +
617T ARG* 1.3 57.5 + - - +
619T MET* 4.0 1.6 - - - +
620T ALA* 2.9 33.3 + - - +
627T VAL* 3.8 6.5 - - + +
630T ALA* 3.6 15.2 - - + +
631T ARG* 3.4 42.2 - - + +
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Residues in contact with ARG 617 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613T LYS* 3.0 22.3 + - + +
614T ALA* 3.5 11.9 - - - +
616T ALA* 1.3 75.4 - - - +
618T ILE* 1.3 55.4 + - + +
620T ALA* 4.1 4.2 - - - +
621T ASP* 2.7 80.3 + - - +
627T VAL* 3.8 37.5 - - + +
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Residues in contact with ILE 618 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605T ILE* 4.6 24.9 - - + +
606T ILE* 4.8 7.6 - - + -
614T ALA* 3.2 15.0 + - + +
615T ARG* 3.1 10.9 + - - +
617T ARG* 1.3 75.7 - - + +
619T MET* 1.3 61.9 + - - +
622T ASP* 2.8 52.3 + - + +
623T TYR* 3.4 23.2 + - + -
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Residues in contact with MET 619 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597T VAL* 5.6 1.8 - - - -
606T ILE* 3.7 33.4 - - + -
615T ARG* 2.9 56.4 + - + +
616T ALA 4.0 3.4 - - - +
618T ILE* 1.3 75.7 - - - +
620T ALA* 1.3 58.3 + - - +
623T TYR* 3.2 25.1 + - - +
625T TRP* 2.9 52.6 + - + +
630T ALA* 4.0 21.5 - - + +
633T ILE* 4.0 15.9 - - + -
636T PHE* 5.3 1.8 - - + -
645T LEU* 5.1 7.0 - - - -
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Residues in contact with ALA 620 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616T ALA 2.9 18.4 + - - +
617T ARG* 4.0 9.4 - - - +
619T MET* 1.3 76.6 - - - +
621T ASP* 1.3 65.7 + - - +
624T GLY* 3.3 19.8 + - - -
625T TRP* 3.0 24.6 - - + +
627T VAL* 3.7 27.1 - - + +
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Residues in contact with ASP 621 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617T ARG* 2.7 67.9 + - - +
620T ALA* 1.3 74.4 - - - +
622T ASP* 1.3 67.4 + - - +
624T GLY 5.0 0.2 + - - -
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Residues in contact with ASP 622 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618T ILE* 2.8 39.8 + - + +
621T ASP* 1.3 81.8 - - - +
623T TYR* 1.3 76.2 + - + +
624T GLY 3.6 1.3 - - - -
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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