Contacts of the helix formed by residues 788 - 800 (chain A) in PDB entry 3AR2
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 ILE 788 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR* 5.5 2.5 - - + -
294A TYR* 3.7 15.9 - - + +
298A ILE* 5.2 2.2 - - - -
785A GLU* 5.7 0.7 - - + -
787A LEU* 1.3 80.6 - - - +
789A PRO* 1.4 80.0 - - + +
790A VAL* 3.8 19.1 - - + -
791A GLN* 2.9 47.2 + - + +
792A LEU* 3.0 16.2 + - - +
897A MET* 3.9 17.3 - - + -
957A PHE 4.4 0.2 - - - +
958A LYS* 3.7 24.0 - - + -
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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
----------------------------------------------------------
90A GLU* 3.4 21.1 - - - +
294A TYR* 3.9 15.3 - - + -
297A LYS* 4.2 26.9 - - + +
298A ILE* 3.7 28.7 - - + -
301A ALA* 3.9 11.7 - - + +
788A ILE* 1.4 90.8 - - + +
790A VAL* 1.3 64.7 + - + +
792A LEU* 3.0 14.1 + - + +
793A LEU* 3.1 18.3 + - - +
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Residues in contact with VAL 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.5 31.9 - - + +
89A VAL* 4.6 9.2 - - + -
90A GLU* 3.2 45.8 - - + +
93A VAL* 5.3 2.1 - - + +
788A ILE* 3.8 19.7 - - + -
789A PRO* 1.3 77.7 - - + +
791A GLN* 1.3 59.7 + - - +
793A LEU* 3.2 8.6 + - + +
794A TRP* 2.8 32.8 + - - +
956A ILE 4.4 5.2 - - - +
957A PHE* 4.6 18.4 - - + -
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Residues in contact with GLN 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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787A LEU* 3.5 29.4 - - + +
788A ILE* 2.9 33.2 + - + +
790A VAL* 1.3 79.8 - - - +
792A LEU* 1.3 60.8 + - - +
794A TRP* 4.1 2.6 - - - +
795A VAL* 3.4 7.1 + - - +
897A MET* 3.8 20.5 - - - +
901A LEU* 3.0 49.4 - - + +
957A PHE* 3.1 28.8 + - + +
958A LYS* 3.2 17.4 + - - +
959A LEU* 3.4 10.8 - - - +
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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
----------------------------------------------------------
298A ILE* 3.7 17.0 - - + +
301A ALA* 3.6 30.7 - - + +
302A LEU* 3.7 24.2 - - + +
305A ALA* 4.6 5.6 - - + +
771A GLU* 5.9 4.0 - - + +
775A ILE* 4.1 20.4 - - + -
787A LEU* 3.5 30.5 - - + -
788A ILE 3.0 16.0 + - - +
789A PRO* 3.0 7.4 + - + +
791A GLN* 1.3 74.5 - - - +
793A LEU* 1.3 56.6 + - - +
794A TRP 3.1 1.1 - - - -
795A VAL* 2.9 14.2 - - + +
796A ASN* 2.7 35.5 + - - +
904A LEU* 5.7 0.7 - - + -
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Residues in contact with LEU 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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72A SER* 5.5 0.9 - - - +
90A GLU* 3.7 45.3 - - + +
93A VAL* 3.4 22.9 - - + +
94A ILE* 3.2 32.3 - - + -
301A ALA* 3.6 33.7 - - + +
304A VAL* 4.4 6.3 - - + -
789A PRO 3.1 10.7 + - - +
790A VAL* 3.6 8.1 - - + +
792A LEU* 1.3 74.6 - - - +
794A TRP* 1.3 57.7 + - - +
796A ASN* 2.9 10.0 + - + +
797A LEU 2.9 25.5 + - - -
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Residues in contact with TRP 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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93A VAL* 3.9 12.2 - - + +
96A LEU* 6.1 2.5 - - + -
790A VAL 2.8 16.6 + - - +
791A GLN* 4.1 6.3 - - - +
793A LEU* 1.3 72.7 - - - +
795A VAL* 1.3 71.1 + - - +
796A ASN 3.0 0.9 + - - -
797A LEU* 3.0 20.8 + - + +
798A VAL* 3.0 40.0 + - + +
901A LEU* 4.1 12.8 - - + -
905A VAL* 4.7 2.7 - - + +
943A LEU* 3.1 50.5 - - + -
944A HIS* 2.8 34.6 + + - -
947A ILE* 3.2 28.9 - - + +
957A PHE* 3.4 33.4 - + + -
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Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 5.2 1.1 - - + -
771A GLU* 4.3 15.9 - - + +
791A GLN 3.4 10.9 + - - +
792A LEU* 2.9 30.7 + - + +
794A TRP* 1.3 78.2 - - - +
796A ASN* 1.3 59.2 + - - +
798A VAL* 4.6 0.2 - - - -
799A THR* 2.4 48.5 + - + +
901A LEU* 3.8 7.4 - - + -
904A LEU* 3.7 36.1 - - + -
905A VAL* 3.8 29.4 - - + +
908A GLU* 4.2 3.8 - - - +
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Residues in contact with ASN 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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93A VAL 4.4 4.4 + - - -
94A ILE* 5.0 0.4 - - - +
97A ILE* 4.3 13.3 - - - +
304A VAL* 2.8 27.0 - - - +
305A ALA* 3.4 13.2 - - - +
309A GLU* 2.8 28.4 + - - +
771A GLU* 5.5 0.7 - - - -
792A LEU 2.7 12.8 + - - +
793A LEU* 2.9 17.7 + - - +
794A TRP 3.0 0.4 + - - -
795A VAL* 1.3 76.9 - - - +
797A LEU* 1.3 71.0 + - - +
798A VAL 2.8 2.8 + - - -
800A ASP* 2.7 43.2 + - - +
996A CA 2.8 10.7 - - - -
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Residues in contact with LEU 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.5 29.6 - - + +
96A LEU* 3.4 46.2 - - + -
97A ILE* 3.7 26.1 - - + +
793A LEU 2.9 17.6 + - - +
794A TRP* 3.7 19.5 - - + +
796A ASN* 1.3 72.8 - - - +
798A VAL* 1.3 78.9 + - + +
800A ASP 4.4 0.7 - - - -
801A GLY* 4.0 15.8 + - - -
802A LEU 5.2 0.3 + - - -
803A PRO* 5.3 0.7 - - - +
940A SER* 5.0 1.0 + - - -
943A LEU* 5.0 9.0 - - + -
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Residues in contact with VAL 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A TRP* 3.0 43.9 + - + +
795A VAL* 4.1 3.1 - - - +
796A ASN 2.8 0.2 + - - -
797A LEU* 1.3 97.6 - - + +
799A THR* 1.3 59.0 + - + +
803A PRO* 3.5 5.4 - - - +
905A VAL* 3.7 31.6 - - + -
909A MET* 3.4 10.6 - - - +
940A SER* 3.1 44.7 + - - +
943A LEU* 5.0 4.9 - - + -
944A HIS* 5.0 0.4 - - + -
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Residues in contact with THR 799 (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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763A TYR* 2.9 32.2 + - - -
771A GLU* 3.9 1.4 + - - -
795A VAL* 2.4 38.6 + - + +
796A ASN 3.4 0.9 + - - -
798A VAL* 1.3 82.1 - - + +
800A ASP* 1.3 57.6 + - - +
801A GLY 3.5 4.4 + - - -
803A PRO* 4.4 3.5 - - - +
804A ALA* 4.3 1.0 - - - +
905A VAL* 4.0 11.0 - - + -
908A GLU* 3.0 45.0 + - + +
909A MET* 3.7 13.0 - - + -
995A CA 2.5 19.1 - - - -
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Residues in contact with ASP 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.0 19.7 - - - +
101A ASN* 4.6 3.8 + - - -
305A ALA 3.0 9.2 - - - +
309A GLU* 3.7 10.8 - - - +
310A GLY* 5.0 3.3 + - - -
763A TYR* 5.0 0.9 - - - -
764A LEU* 3.5 22.6 - - + +
767A SER* 5.3 0.3 - - - -
768A ASN* 3.0 8.4 - - - +
771A GLU* 4.7 0.2 - - - +
796A ASN* 2.7 27.1 + - - +
799A THR* 1.3 75.5 + - - +
801A GLY* 1.3 57.3 + - - +
804A ALA* 4.3 10.7 - - - +
995A CA 2.7 26.6 - - - -
996A CA 2.6 29.1 - - - -
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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
------------------------------------------------------------
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