Contacts of the helix formed by residues 986 - 997 (chain B) in PDB entry 6AHU
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 SER 986 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711B LEU* 4.5 12.0 - - - +
712B THR* 4.0 16.7 - - - +
715B TRP* 4.8 10.6 - - - -
855B ALA 3.6 19.1 + - - -
856B LEU* 4.4 2.9 - - - +
857B VAL* 5.0 2.2 - - - -
964B LEU* 4.4 6.3 + - - +
985B VAL* 1.3 78.4 - - - +
987B LEU* 1.3 65.3 + - - +
988B THR* 4.3 12.3 - - - -
989B GLY* 3.7 9.7 + - - +
990B LEU* 3.4 26.9 + - - +
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Residues in contact with LEU 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B LEU* 3.7 20.2 - - + -
815B LEU* 3.8 30.1 - - + -
848B ILE* 4.8 11.4 - - + +
849B LEU* 3.7 23.1 - - + -
852B PHE* 4.6 7.9 - - + +
855B ALA* 3.7 30.2 + - + -
856B LEU 5.1 0.2 - - - +
857B VAL* 3.7 25.6 - - + -
986B SER* 1.3 73.4 - - - +
988B THR* 1.3 61.5 + - + +
990B LEU* 3.1 11.6 + - + +
991B LEU* 2.9 36.4 + - + +
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Residues in contact with THR 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B TRP* 3.3 47.2 - - - +
716B GLU* 5.5 4.0 - - + -
719B VAL* 4.7 15.7 - - + +
849B LEU* 3.7 35.4 - - + -
986B SER* 4.4 4.0 - - - -
987B LEU* 1.3 77.0 - - + +
989B GLY* 1.3 62.3 + - - +
991B LEU* 4.6 1.1 - - - +
992B ASP* 3.3 24.8 + - - +
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Residues in contact with GLY 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B TRP* 4.2 21.3 - - - -
877B VAL* 5.0 2.6 - - - +
964B LEU* 3.4 31.7 - - - +
986B SER* 3.7 10.9 + - - -
987B LEU 3.2 0.4 - - - -
988B THR* 1.3 83.7 + - - +
990B LEU* 1.3 60.2 + - - +
992B ASP* 4.3 1.6 - - - +
993B MET* 3.6 15.6 + - - +
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Residues in contact with LEU 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B LEU* 5.7 7.9 - - + -
819B CYS* 4.8 13.5 - - - -
857B VAL* 5.2 7.2 - - + -
859B VAL* 4.5 11.9 - - + -
964B LEU* 4.8 6.3 - - + -
985B VAL* 3.8 28.5 - - + -
986B SER 3.4 14.5 + - - +
987B LEU* 3.1 18.6 + - + +
989B GLY* 1.3 77.9 - - - +
991B LEU* 1.3 55.0 + - + +
993B MET* 2.9 8.9 + - + +
994B LEU* 2.7 47.9 + - + +
1020B ILE* 4.6 20.6 - - + -
1022B ILE* 4.7 9.9 - - + -
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Residues in contact with LEU 991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B LEU* 4.8 17.0 - - + -
818B TRP* 5.4 4.0 - - + -
845B CYS* 3.7 50.5 - - + +
848B ILE* 5.4 7.2 - - + -
849B LEU* 3.8 31.2 - - + -
987B LEU* 2.9 24.4 + - + +
988B THR* 4.9 0.7 - - - -
990B LEU* 1.3 73.9 - - + +
992B ASP* 1.3 57.1 + - - +
994B LEU* 3.8 26.4 - - + +
995B SER* 3.3 26.2 + - - -
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Residues in contact with ASP 992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B TRP* 4.8 6.3 - - + -
718B ARG* 4.1 27.9 + - - -
719B VAL* 5.7 6.9 - - + +
988B THR 3.3 19.9 + - - +
989B GLY* 4.3 4.0 - - - +
990B LEU 3.2 0.8 - - - -
991B LEU* 1.3 77.1 - - - +
993B MET* 1.3 62.5 + - - +
995B SER* 4.2 4.6 - - - -
996B SER* 3.6 18.2 + - - -
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Residues in contact with MET 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B VAL* 3.7 32.3 - - + -
878B PRO* 3.8 17.7 - - + +
883B PHE* 3.7 36.8 - - + -
964B LEU* 5.7 1.6 - - + -
989B GLY 3.6 12.5 + - - +
990B LEU* 2.9 10.1 + - + +
992B ASP* 1.3 77.3 - - - +
994B LEU* 1.3 65.7 + - + +
996B SER* 3.2 18.9 + - - +
997B GLN* 3.5 25.9 + - + +
1002B ARG 4.7 11.4 - - - +
1005B VAL* 4.6 15.5 - - + -
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Residues in contact with LEU 994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B LEU* 5.5 4.3 - - + -
818B TRP* 3.8 23.4 - - + +
819B CYS* 3.7 35.2 - - - -
840B LEU* 5.9 1.9 - - - +
990B LEU* 2.7 29.1 + - + +
991B LEU* 3.8 29.4 - - + +
993B MET* 1.3 76.3 - - + +
995B SER* 1.3 61.0 + - - +
997B GLN* 3.5 10.1 - - - +
998B PRO* 4.4 0.7 - - - +
1002B ARG* 2.9 59.0 + - + +
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Residues in contact with SER 995 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840B LEU* 6.5 0.2 - - - -
842B ARG* 2.6 65.9 + - - +
991B LEU 3.3 20.8 + - - -
992B ASP* 4.2 6.1 - - - -
993B MET 3.3 0.2 - - - -
994B LEU* 1.3 77.5 - - - +
996B SER* 1.3 61.4 + - - +
997B GLN 3.3 0.4 + - - -
998B PRO* 4.0 0.5 - - - +
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Residues in contact with SER 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B LYS* 5.4 8.1 - - - +
992B ASP 3.6 11.0 + - - -
993B MET* 3.2 18.4 + - - +
995B SER* 1.3 79.3 - - - +
997B GLN* 1.3 75.1 + - - +
998B PRO* 3.6 7.5 - - - +
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Residues in contact with GLN 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B LYS* 6.0 4.4 - - - +
883B PHE* 3.7 39.1 - - + -
993B MET* 3.5 23.5 + - + +
994B LEU 3.5 4.0 + - - +
995B SER 3.3 1.0 - - - -
996B SER* 1.3 95.7 + - - +
998B PRO* 1.3 57.9 - - - +
999B ALA* 3.3 11.7 - - - +
1000B ALA 3.8 14.8 - - - +
1001B GLN 5.1 1.6 - - - +
1002B ARG* 2.7 53.7 + - + +
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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