Contacts of the helix formed by residues 786 - 798 (chain A) in PDB entry 5C53
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 ALA 786 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784A GLY 3.7 0.8 + - - -
785A GLY* 1.3 71.1 - - - -
787A SER* 1.3 62.8 + - - +
788A GLY 3.3 2.0 - - - -
789A PRO* 3.5 16.2 - - + +
790A ARG* 3.3 24.6 + - - +
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Residues in contact with SER 787 (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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462A SER* 4.5 11.6 + - - -
466A LEU* 6.0 1.4 - - - +
603A MET* 4.8 10.9 - - - +
783A PRO 5.1 1.5 + - - -
784A GLY 3.8 26.2 + - - -
785A GLY 3.3 1.8 - - - -
786A ALA* 1.3 77.5 - - - +
788A GLY* 1.3 60.2 + - - +
790A ARG* 3.6 5.0 + - - +
791A ALA* 2.9 31.2 + - - +
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Residues in contact with GLY 788 (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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603A MET* 5.2 4.0 - - - +
774A MET* 3.8 20.9 - - - -
781A ALA* 4.2 15.8 - - - +
784A GLY 5.8 0.2 - - - -
785A GLY 4.5 2.4 + - - -
787A SER* 1.3 77.5 - - - +
789A PRO* 1.3 65.1 - - - +
791A ALA* 2.8 23.8 + - - +
792A LEU* 2.9 16.5 + - - +
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Residues in contact with PRO 789 (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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771A LEU* 4.0 3.9 - - + +
774A MET* 3.7 24.4 - - + +
775A GLU* 3.9 31.9 - - + +
780A GLN* 6.3 0.4 - - + -
781A ALA 5.9 0.9 - - - +
785A GLY 4.5 3.8 - - - +
786A ALA* 3.5 25.8 - - + +
788A GLY* 1.3 88.5 - - - +
790A ARG* 1.3 57.1 + - - +
792A LEU* 3.5 8.5 + - + +
793A GLU* 2.9 33.2 + - - +
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Residues in contact with ARG 790 (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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455A LEU* 4.3 12.7 - - - +
458A GLU* 3.8 30.6 + - - +
786A ALA 3.3 19.5 + - - +
787A SER* 3.8 6.1 - - - +
788A GLY 3.1 1.0 - - - -
789A PRO* 1.3 76.0 - - - +
791A ALA* 1.3 60.9 + - - +
793A GLU* 3.2 14.3 + - - +
794A ILE* 2.9 53.3 + - + +
797A MET* 5.0 12.0 - - - +
271B SER* 4.9 14.7 + - - +
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Residues in contact with ALA 791 (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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459A MET* 6.0 3.6 - - + +
463A LEU* 5.7 7.0 - - + -
594A LEU* 4.6 17.2 - - + +
603A MET* 5.9 6.5 - - + -
787A SER* 2.9 15.1 + - - +
788A GLY* 2.8 12.3 + - - +
790A ARG* 1.3 74.3 - - - +
792A LEU* 1.3 64.3 + - + +
794A ILE* 3.2 13.3 + - - +
795A ASN* 2.9 27.9 + - - +
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Residues in contact with LEU 792 (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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594A LEU* 6.3 0.2 - - + -
766A PHE* 6.3 1.6 - - + -
767A ALA 3.4 26.2 - - - +
768A LYS* 3.7 40.2 - - + +
769A ASP 4.7 0.2 - - - +
770A PHE 5.1 2.9 - - - +
771A LEU* 3.6 26.5 - - + +
774A MET* 4.4 24.7 - - + -
788A GLY* 2.9 22.2 + - - +
789A PRO* 3.7 7.6 - - + +
791A ALA* 1.3 80.5 - - + +
793A GLU* 1.3 58.1 + - - +
795A ASN* 3.4 5.6 + - + +
796A LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 793 (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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771A LEU* 4.2 18.5 - - + +
775A GLU* 4.2 8.6 - - - +
789A PRO 2.9 20.0 + - - +
790A ARG* 3.2 21.3 + - - +
792A LEU* 1.3 74.7 - - - +
794A ILE* 1.3 59.0 + - - +
796A LYS* 3.2 15.4 + - - +
797A MET* 2.9 48.7 + - + +
868A ASP* 4.0 13.3 - - - +
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Residues in contact with ILE 794 (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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455A LEU* 3.9 31.9 - - + +
458A GLU* 3.4 38.1 - - + +
459A MET* 3.9 23.6 - - + +
790A ARG* 2.9 43.8 + - + +
791A ALA* 3.5 10.8 - - - +
793A GLU* 1.3 74.2 - - - +
795A ASN* 1.3 63.6 + - - +
797A MET* 3.3 9.6 + - - +
798A ILE* 3.3 29.7 + - + +
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Residues in contact with ASN 795 (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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459A MET* 5.7 2.0 - - - -
594A LEU* 3.4 25.2 - - + +
595A GLN* 2.4 33.9 + - - +
768A LYS* 3.3 32.4 - - + +
791A ALA 2.9 13.8 + - - +
792A LEU* 3.6 11.4 - - + +
794A ILE* 1.3 78.6 - - - +
796A LYS* 1.3 55.7 + - - +
798A ILE* 4.4 2.7 - - - -
799A SER* 2.3 41.1 + - - -
802A ARG* 3.0 16.6 + - - +
21P G 4.6 2.9 + - - +
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Residues in contact with LYS 796 (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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768A LYS 5.3 2.9 - - - +
769A ASP* 4.6 15.3 - - - +
771A LEU* 3.4 42.3 - - + +
772A PRO* 5.9 0.2 - - - +
792A LEU 2.9 15.2 + - - +
793A GLU* 3.2 17.6 + - - +
795A ASN* 1.3 78.9 + - - +
797A MET* 1.3 62.4 + - - +
799A SER* 3.4 17.4 + - - -
868A ASP* 3.1 31.2 - - - +
869A ARG* 4.3 13.8 + - - +
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Residues in contact with MET 797 (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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455A LEU* 4.0 31.9 - - + -
790A ARG* 5.0 11.7 - - - +
793A GLU* 2.9 41.3 + - + +
794A ILE* 3.6 8.5 - - - +
795A ASN 3.2 0.2 - - - -
796A LYS* 1.3 79.4 - - - +
798A ILE* 1.3 57.7 + - - +
799A SER 3.2 2.4 + - - -
800A PHE 4.4 2.6 + - - -
801A TRP 5.1 0.7 + - - -
868A ASP* 3.3 32.1 - - - +
869A ARG* 3.6 4.9 - - - +
870A VAL* 3.2 28.2 + - + +
1198A LYS* 6.1 6.7 - - + -
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Residues in contact with ILE 798 (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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452A TYR* 3.7 36.1 - - + +
455A LEU* 3.8 34.8 - - + -
456A GLN* 4.6 11.0 - - + -
459A MET* 4.4 24.5 - - + -
794A ILE* 3.3 23.5 + - + +
795A ASN 4.0 0.4 - - - +
797A MET* 1.3 75.4 - - - +
799A SER* 1.3 63.8 + - - +
800A PHE 3.3 2.7 - - - -
801A TRP 4.0 2.9 - - - +
802A ARG* 3.0 46.5 + - - +
870A VAL* 3.9 9.4 - - + -
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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