Contacts of the helix formed by residues 772 - 787 (chain D) in PDB entry 4PE5
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 TRP 772 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403D ASP* 3.8 25.8 - - + -
404D ASP* 4.7 4.9 - - + -
406D LEU* 6.0 6.8 - - + +
472D VAL* 4.0 26.7 - - + -
473D LYS 4.5 4.5 - - - -
474D PHE* 4.0 34.1 - + + -
507D TYR* 3.2 42.8 + + + -
508D MET* 5.3 9.6 - - - -
766D ILE* 4.4 5.4 - - + -
770D SER* 3.4 9.5 + - - +
771D GLY* 1.3 83.6 - - - +
773D LYS* 1.3 59.4 + - - +
774D ARG 3.3 2.5 - - - -
775D GLN* 3.8 10.9 - - + +
776D VAL* 2.9 44.4 + - + +
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Residues in contact with LYS 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D ASP* 5.3 10.3 - - + +
525D PHE 5.8 4.3 - - - +
526D SER* 5.2 7.1 - - - +
766D ILE* 3.7 25.8 - - + +
770D SER 5.4 6.5 - - - +
771D GLY 3.6 0.8 - - - -
772D TRP* 1.3 77.9 - - - +
774D ARG* 1.3 57.8 + - - +
776D VAL* 4.0 3.5 - - - +
777D ASP* 2.9 32.1 + - - +
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Residues in contact with ARG 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 5.5 11.4 - - + -
771D GLY 4.9 4.6 + - - +
772D TRP 3.3 0.4 - - - +
773D LYS* 1.3 78.3 - - - +
775D GLN* 1.3 59.6 + - - +
777D ASP* 3.3 6.0 + - - +
778D LEU* 2.9 41.5 + - + +
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Residues in contact with GLN 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D SER* 4.4 6.9 + - - -
472D VAL* 3.7 35.7 + - + +
771D GLY 4.9 4.6 + - - +
772D TRP* 3.4 20.8 + - + +
774D ARG* 1.3 78.7 - - - +
776D VAL* 1.3 57.8 + - - +
778D LEU* 3.4 16.2 + - - +
779D ALA* 2.9 29.9 + - - +
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Residues in contact with VAL 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 4.3 19.3 - - + -
472D VAL* 5.0 12.3 - - + -
474D PHE* 5.2 5.4 - - + -
508D MET* 4.0 23.6 - - + -
526D SER* 4.0 13.5 - - - +
764D ILE* 4.6 5.8 - - + -
766D ILE* 5.7 3.4 - - + -
772D TRP* 2.9 31.4 + - + +
773D LYS* 4.0 3.8 - - - +
775D GLN* 1.3 72.1 - - + +
777D ASP* 1.3 61.2 + - - +
779D ALA* 3.1 8.0 + - - +
780D ILE* 2.9 47.2 + - + +
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Residues in contact with ASP 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D SER* 4.8 2.0 - - - -
527D VAL* 3.5 30.7 - - + +
773D LYS 2.9 20.6 + - - +
774D ARG* 3.6 6.3 - - - +
776D VAL* 1.3 77.6 - - - +
778D LEU* 1.3 59.2 + - + +
780D ILE* 3.3 1.3 + - - -
781D LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 778 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ASN* 3.1 19.1 - - - +
524A ALA* 3.6 44.2 - - + +
525A GLN* 3.7 30.7 - - + +
774D ARG* 2.9 26.5 + - + +
775D GLN* 3.7 16.4 - - - +
777D ASP* 1.3 78.0 - - + +
779D ALA* 1.3 58.3 + - - +
781D LEU* 4.5 2.2 - - - -
782D GLN* 2.9 25.5 + - - +
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Residues in contact with ALA 779 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ILE* 4.3 17.3 - - + +
471D SER* 3.8 27.8 - - - +
472D VAL* 5.1 4.0 - - + +
775D GLN* 2.9 15.6 + - - +
776D VAL* 3.1 12.8 + - - +
778D LEU* 1.3 74.9 - - - +
780D ILE* 1.3 60.0 + - - +
782D GLN* 3.1 8.1 + - - +
783D LEU* 2.9 35.0 + - + +
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Residues in contact with ILE 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 5.3 3.8 - - + -
468D ILE* 4.1 16.4 - - + -
526D SER* 3.6 26.9 - - - +
527D VAL* 3.6 26.0 - - + +
529D PHE* 4.0 28.7 - - + -
764D ILE* 4.5 11.0 - - + -
776D VAL* 2.9 29.1 + - + +
777D ASP 3.8 3.8 - - - +
779D ALA* 1.3 74.8 - - - +
781D LEU* 1.3 58.1 + - - +
783D LEU* 3.0 13.2 + - - +
784D PHE* 2.9 31.9 + - + -
789D MET* 4.2 7.6 - - + -
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Residues in contact with LEU 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 3.6 38.6 - - + +
520A ASN* 3.5 19.8 - - - +
521A ASN* 3.6 25.1 + - - +
524A ALA* 3.6 19.5 - - + -
527D VAL* 3.7 20.4 - - + -
777D ASP* 2.9 25.7 + - + +
778D LEU* 4.0 2.0 - - - +
780D ILE* 1.3 75.9 - - - +
782D GLN* 1.3 57.8 + - - +
784D PHE* 3.2 27.6 + - + +
785D GLY* 2.9 22.9 + - - -
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Residues in contact with GLN 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ASN* 3.4 23.3 - - - +
471D SER* 5.6 3.4 - - - +
778D LEU 2.9 20.5 + - - +
779D ALA* 3.2 11.7 - - - +
781D LEU* 1.3 75.8 - - - +
783D LEU* 1.3 59.8 + - + +
785D GLY* 3.8 1.0 - - - +
786D ASP* 2.9 31.7 + - - +
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Residues in contact with LEU 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 4.2 14.6 - - + -
467D LYS* 4.0 36.6 - - + +
468D ILE* 4.5 15.0 - - + -
471D SER* 5.4 4.9 - - - +
779D ALA* 2.9 25.7 + - + +
780D ILE* 3.0 13.0 + - - +
782D GLN* 1.3 77.7 - - + +
784D PHE* 1.3 63.2 + - - +
786D ASP* 4.6 4.0 - - + -
787D GLY 3.2 16.3 + - - -
788D GLU* 3.4 22.2 + - + -
789D MET* 3.5 31.0 + - + +
792D LEU* 5.0 3.6 - - + -
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Residues in contact with PHE 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ILE 5.5 1.1 - - - +
520A ASN* 6.0 0.7 - - - -
692A TYR* 4.3 0.2 - - - -
754A PHE* 3.4 32.4 - - + -
755A ARG* 4.0 26.0 - - + -
756A SER* 4.6 16.4 - - - -
527D VAL* 4.4 4.5 - - + -
528D PRO 3.3 26.9 - - - -
529D PHE* 3.6 15.9 - - - -
780D ILE* 2.9 12.8 + - + -
781D LEU* 3.2 36.8 + - + +
783D LEU* 1.3 77.7 - - - +
785D GLY* 1.3 61.7 + - - +
787D GLY* 3.4 12.1 + - - -
789D MET* 3.4 41.0 - - + +
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Residues in contact with GLY 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A ASN* 6.2 1.8 - - - -
521A ASN* 5.7 2.2 - - - -
522A GLU* 5.5 9.2 - - - -
692A TYR* 3.7 20.3 - - - +
695A ARG 5.1 4.5 - - - +
696A GLN* 3.8 8.3 - - - +
754A PHE* 4.0 11.6 - - - -
781D LEU 2.9 14.2 + - - -
782D GLN* 3.3 3.6 + - - -
784D PHE* 1.3 75.7 - - - +
786D ASP* 1.3 63.7 + - - +
787D GLY 3.4 0.5 + - - -
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Residues in contact with ASP 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A ARG 6.0 0.9 - - - -
696A GLN* 3.0 25.2 + - - +
698A GLU* 4.8 2.3 - - - +
782D GLN 2.9 17.7 + - - +
783D LEU* 4.1 6.1 - - + +
785D GLY* 1.3 76.7 - - - +
787D GLY* 1.3 59.9 + - - +
788D GLU* 3.3 10.5 - - + +
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Residues in contact with GLY 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A TYR* 4.9 11.2 - - - -
696A GLN* 4.9 0.7 - - - -
783D LEU 3.2 5.8 + - - -
784D PHE 3.4 9.6 + - - -
785D GLY 3.2 3.6 - - - -
786D ASP* 1.3 78.8 - - - +
788D GLU* 1.3 62.6 + - - +
789D MET* 3.1 3.8 - - - -
790D GLU* 3.3 20.3 + - - +
791D GLU* 3.6 8.7 + - - +
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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