Contacts of the helix formed by residues 779 - 788 (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 GLY 779 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535T GLU* 5.3 5.8 - - - -
777T SER 3.3 2.0 + - - -
778T PHE* 1.3 71.4 - - - +
780T PHE* 1.3 65.1 + - - +
781T THR* 3.3 8.8 - - - +
782T GLY* 2.9 15.1 + - - -
783T GLU* 3.1 20.2 + - - +
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Residues in contact with PHE 780 (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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731T VAL* 4.3 11.4 - - + -
733T ILE* 4.2 18.6 - - + -
743T ILE* 6.1 0.4 - - + -
746T VAL* 3.7 28.9 - - + -
747T LEU* 4.2 19.3 - - + -
750T LYS* 4.3 15.0 - - + +
772T LEU* 3.8 25.4 - - + -
776T GLU 4.3 1.1 - - - +
777T SER* 3.4 25.9 + - - +
778T PHE 3.2 3.4 + - - -
779T GLY* 1.3 76.8 - - - +
781T THR* 1.3 68.9 + - - +
782T GLY 3.0 0.3 + - - -
783T GLU* 3.1 6.3 + - - +
784T LEU* 2.9 48.3 + - + +
794T PRO* 4.0 13.7 - - + -
796T MET* 4.5 9.6 - - - -
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Residues in contact with THR 781 (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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484T SER* 5.8 3.6 - - - -
488T VAL* 4.5 16.6 - - - +
489T VAL* 4.4 14.6 - - + -
533T THR 5.6 0.7 + - - -
534T GLY* 5.9 0.2 - - - -
535T GLU* 3.6 30.1 + - + +
777T SER 5.0 0.4 + - - -
779T GLY* 4.6 6.7 - - - +
780T PHE* 1.3 86.9 - - - +
782T GLY* 1.3 63.4 + - - +
784T LEU* 3.9 5.3 - - - +
785T ARG* 3.4 22.9 + - - +
794T PRO* 4.2 18.4 - - - +
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Residues in contact with GLY 782 (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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535T GLU* 4.2 9.6 - - - -
779T GLY* 2.9 9.2 + - - -
781T THR* 1.3 83.7 - - - +
783T GLU* 1.3 63.8 + - - +
784T LEU 3.1 1.8 - - - -
785T ARG* 3.0 46.7 + - - +
786T GLN* 3.1 5.4 + - - +
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Residues in contact with GLU 783 (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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746T VAL* 3.6 17.6 - - + +
749T LYS* 5.1 11.1 - - - +
750T LYS* 2.9 38.1 + - - -
778T PHE 5.3 1.9 - - - +
779T GLY* 3.1 12.9 + - - +
780T PHE 3.1 6.8 + - - +
782T GLY* 1.3 74.6 - - - +
784T LEU* 1.3 57.7 + - - +
786T GLN* 3.7 8.2 + - - +
787T ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 784 (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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733T ILE* 4.1 9.2 - - + -
743T ILE* 4.0 22.7 - - + -
746T VAL* 4.2 10.5 - - + +
780T PHE* 2.9 38.9 + - + +
781T THR 3.9 4.7 - - - +
783T GLU* 1.3 74.3 - - - +
785T ARG* 1.3 66.2 + - - +
786T GLN 3.1 1.6 - - - -
787T ALA 3.1 1.4 + - - -
788T THR* 2.9 44.9 + - + +
792T ALA* 3.7 20.2 - - + +
794T PRO* 3.6 43.1 - - + -
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Residues in contact with ARG 785 (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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535T GLU* 5.1 6.1 + - - -
781T THR 3.4 11.8 + - - +
782T GLY* 3.0 33.4 + - - +
784T LEU* 1.3 78.6 - - - +
786T GLN* 1.3 87.9 + - - +
788T THR* 3.8 7.0 - - - -
789T GLY* 2.9 11.1 + - - -
790T GLY* 2.5 41.1 + - - +
792T ALA 5.1 6.7 + - - +
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Residues in contact with GLN 786 (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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782T GLY 3.1 13.6 + - - +
783T GLU* 3.7 9.2 - - - +
784T LEU 3.1 0.6 - - - -
785T ARG* 1.3 106.3 + - - +
787T ALA* 1.3 57.2 + - - +
788T THR 3.4 0.2 - - - -
789T GLY* 4.1 4.7 + - - -
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Residues in contact with ALA 787 (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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739T ALA 4.8 0.3 - - - +
742T GLY* 3.3 24.8 - - - +
745T SER* 5.3 4.5 - - - +
746T VAL* 3.4 23.3 - - + -
783T GLU 3.1 17.2 + - - +
784T LEU 3.1 3.6 + - - +
786T GLN* 1.3 76.5 - - - +
788T THR* 1.3 61.1 + - - +
789T GLY 3.6 0.4 - - - -
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Residues in contact with THR 788 (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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739T ALA* 3.8 28.6 - - - +
743T ILE* 4.2 10.5 - - + +
784T LEU* 2.9 30.1 + - + +
785T ARG* 3.7 1.7 + - - -
787T ALA* 1.3 81.1 - - - +
789T GLY* 1.3 63.8 + - - +
790T GLY 3.6 1.7 + - - -
791T GLN* 3.2 27.8 + - - +
792T ALA* 3.0 42.9 + - + +
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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