Contacts of the helix formed by residues 793 - 807 (chain A) in PDB entry 3L7A
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 ASN 793 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A ALA 4.8 3.4 - - - +
790A LEU* 3.0 15.7 + - + +
792A LYS* 1.3 78.9 - - - +
794A PRO* 1.4 65.5 - - - +
795A ARG* 3.5 8.7 + - - +
796A GLU* 3.3 35.8 + - + +
797A TRP 2.9 18.4 + - - -
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Residues in contact with PRO 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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791A TYR 4.0 7.8 - - - +
792A LYS 3.2 13.0 - - - +
793A ASN* 1.4 84.2 - - - +
795A ARG* 1.3 57.5 + - - +
797A TRP* 3.6 8.2 - - + +
798A THR* 3.0 35.5 + - - +
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Residues in contact with ARG 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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526A ASP* 4.3 12.7 + - - +
528A GLU* 2.8 41.5 + - - +
531A ILE* 3.6 24.3 - - + +
793A ASN* 3.2 8.5 + - - +
794A PRO* 1.3 78.7 - - - +
796A GLU* 1.3 74.1 + - - +
798A THR* 3.4 5.8 + - - -
799A ARG* 3.0 54.2 + - - +
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Residues in contact with GLU 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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790A LEU* 3.9 18.5 - - + +
793A ASN* 3.0 32.7 + - + +
795A ARG* 1.3 93.8 + - + +
797A TRP* 1.3 66.9 + - - +
799A ARG* 2.9 33.1 + - - +
800A MET* 3.1 22.7 + - - +
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Residues in contact with TRP 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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562A LEU* 4.4 3.8 - - + -
661A ASP* 3.4 38.6 + - + +
662A LEU* 4.9 2.9 - - + -
685A GLY 5.2 1.2 + - - -
687A LEU* 3.7 31.8 - - + +
709A PHE* 4.6 2.7 - + - -
787A VAL* 3.7 37.2 - - + -
790A LEU* 3.8 24.0 - - + +
791A TYR* 3.6 50.9 - + + -
793A ASN 2.9 11.6 + - - +
794A PRO* 3.6 13.0 - - + +
796A GLU* 1.3 75.2 - - - +
798A THR* 1.3 62.6 + - - +
800A MET* 3.2 6.1 + - - +
801A VAL* 3.0 43.7 + - + +
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Residues in contact with THR 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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531A ILE* 3.6 36.1 - - + +
534A VAL* 3.9 24.2 - - + -
535A ALA* 3.9 17.7 - - - +
794A PRO 3.0 17.9 + - - -
795A ARG 3.8 4.0 - - - -
797A TRP* 1.3 78.9 - - - +
799A ARG* 1.3 60.1 + - - +
801A VAL* 3.2 7.2 + - + +
802A ILE* 2.9 31.5 + - + +
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Residues in contact with ARG 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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525A VAL* 3.1 36.0 + - + +
526A ASP* 2.8 27.0 + - - -
531A ILE* 3.8 11.0 - - + -
795A ARG* 3.0 50.6 + - - +
796A GLU* 2.9 32.7 + - - +
797A TRP 3.4 0.4 - - - -
798A THR* 1.3 74.6 - - - +
800A MET* 1.3 62.3 - - - +
802A ILE* 3.3 3.7 + - - -
803A ARG* 3.1 54.5 + - - +
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Residues in contact with MET 800 (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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687A LEU* 3.9 16.8 - - + -
706A GLU 3.4 21.1 - - - +
707A ASN* 3.6 42.2 - - - +
708A PHE 5.8 0.2 - - - -
709A PHE* 4.3 11.0 - - + -
790A LEU* 3.6 30.5 - - + -
796A GLU 3.1 12.2 + - - +
797A TRP 3.6 8.1 - - - +
799A ARG* 1.3 73.1 - - - +
801A VAL* 1.3 66.0 + - - +
803A ARG* 3.2 9.4 + - - +
804A ASN* 3.1 26.7 + - - -
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Residues in contact with VAL 801 (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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534A VAL* 4.2 14.6 - - + -
685A GLY* 3.6 41.5 - - - +
687A LEU* 3.8 20.2 - - + -
797A TRP* 3.0 40.0 + - + +
798A THR* 3.4 9.6 - - - +
800A MET* 1.3 75.4 - - - +
802A ILE* 1.3 64.3 + - - +
804A ASN* 2.9 14.3 + - + +
805A ILE* 3.0 23.0 + - + +
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Residues in contact with ILE 802 (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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521A LEU* 4.0 25.5 - - + +
522A LEU* 5.4 1.3 - - + -
524A TYR 4.5 4.0 - - - +
525A VAL* 4.2 16.4 - - + -
530A PHE* 3.9 35.2 - - + -
531A ILE* 3.9 31.4 - - + -
534A VAL* 4.0 13.9 - - + -
798A THR* 2.9 30.7 + - + +
799A ARG* 3.7 9.2 - - - +
800A MET 3.3 0.4 - - - -
801A VAL* 1.3 72.9 - - - +
803A ARG* 1.3 58.1 + - - +
805A ILE* 3.9 6.8 - - + +
806A ALA* 3.0 29.3 + - + +
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Residues in contact with ARG 803 (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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522A LEU* 4.3 21.9 - - + +
525A VAL* 3.9 30.0 - - + +
703A ALA* 4.3 4.2 - - - +
707A ASN* 3.4 39.6 + - - +
799A ARG* 3.1 45.3 + - - +
800A MET* 3.2 10.0 + - - +
802A ILE* 1.3 77.2 - - - +
804A ASN* 1.3 59.6 + - - +
806A ALA* 4.1 0.3 - - - +
807A THR* 3.0 30.5 + - - +
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Residues in contact with ASN 804 (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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682A MET* 3.5 26.8 - - + +
685A GLY* 6.3 0.4 - - - -
686A ALA 4.5 8.3 - - - +
687A LEU* 3.8 17.5 - - + +
688A THR* 4.9 2.6 + - - -
703A ALA* 4.3 3.0 - - - +
707A ASN* 3.0 32.6 + - - +
708A PHE* 3.3 28.7 - - - -
800A MET 3.1 21.0 + - - +
801A VAL* 2.9 13.3 + - + +
803A ARG* 1.3 76.2 - - - +
805A ILE* 1.3 66.3 + - - +
807A THR* 3.1 15.7 + - - -
808A SER* 3.3 10.0 + - - -
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Residues in contact with ILE 805 (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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499A LEU* 4.2 22.9 - - + -
503A ILE* 4.3 12.3 - - + -
518A LEU* 3.4 17.5 - - + +
521A LEU* 4.2 19.7 - - + -
530A PHE* 6.6 0.2 - - + -
534A VAL* 4.6 9.4 - - + -
682A MET 3.7 18.6 + - - +
683A LEU* 4.1 12.1 - - + +
685A GLY* 3.9 16.8 - - - +
801A VAL* 3.0 35.2 + - + +
802A ILE* 4.1 6.3 - - - +
804A ASN* 1.3 74.3 - - - +
806A ALA* 1.3 63.5 + - - +
807A THR 3.2 0.2 + - - -
808A SER* 2.7 22.8 + - - +
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Residues in contact with ALA 806 (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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518A LEU* 3.3 21.9 - - - +
519A ARG* 3.2 31.1 + - - +
521A LEU* 4.0 14.8 - - + +
522A LEU* 3.4 30.7 - - + +
802A ILE 3.0 19.6 + - - +
803A ARG 4.1 0.9 - - - +
804A ASN 3.2 0.2 - - - -
805A ILE* 1.3 76.1 - - - +
807A THR* 1.3 58.8 + - - +
808A SER 3.5 0.4 - - - -
809A GLY 4.9 1.0 + - - -
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Residues in contact with THR 807 (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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519A ARG* 3.9 28.5 - - - +
522A LEU* 4.5 13.9 - - + -
682A MET* 3.7 4.5 - - - +
702A GLU* 3.6 44.2 - - - +
703A ALA* 3.2 22.5 - - - +
803A ARG 3.0 20.2 + - - +
804A ASN 3.1 4.8 + - - -
806A ALA* 1.3 79.8 - - + +
808A SER* 1.3 59.9 + - - +
809A GLY 3.3 3.0 + - - -
810A LYS 4.5 1.2 + - - -
811A PHE* 4.4 1.7 - - - -
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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