Contacts of the helix formed by residues 994 - 1007 (chain A) in PDB entry 7AUD
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 THR 994 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869A LYS* 3.5 33.0 - - + -
871A PRO* 4.2 16.3 - - + +
966A LEU* 4.3 0.4 - - - +
992A PHE 4.2 0.4 + - - -
993A TYR* 1.3 87.9 - - - +
995A TYR* 1.3 62.4 + - - +
996A HIS* 3.4 13.7 + - + +
997A ASP* 3.1 55.1 + - - +
998A VAL* 3.6 2.6 + - - +
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Residues in contact with TYR 995 (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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993A TYR* 3.6 23.4 - - + +
994A THR* 1.3 70.2 + - - +
996A HIS* 1.3 62.2 + - - +
997A ASP 3.1 1.6 - - - -
998A VAL* 2.8 46.7 + - + +
999A THR* 3.0 21.4 + - - -
1002A LYS* 4.2 16.8 + - - -
1024A TYR* 6.0 1.7 - - - -
1027A VAL* 4.7 9.6 - - + -
1031A GLU* 4.4 4.9 - - - -
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Residues in contact with HIS 996 (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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871A PRO* 5.3 15.9 - - + -
994A THR* 3.3 12.3 + - + +
995A TYR* 1.3 78.6 - - - +
997A ASP* 1.3 59.5 + - - +
999A THR* 3.1 17.5 + - + +
1000A ARG* 2.9 46.1 + - + +
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Residues in contact with ASP 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A LYS* 3.0 25.3 + - - +
871A PRO* 6.0 0.9 - - - +
896A LEU* 4.2 2.1 - - + +
965A SER* 3.1 24.8 + - - -
966A LEU* 3.5 18.0 + - + -
992A PHE 4.5 0.2 - - - +
994A THR* 3.1 29.5 + - - +
996A HIS* 1.3 78.3 - - - +
998A VAL* 1.3 59.9 + - - +
1000A ARG* 2.9 31.4 + - - +
1001A LEU* 2.9 33.4 + - - +
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Residues in contact with VAL 998 (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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966A LEU* 3.7 17.3 - - + -
993A TYR* 3.9 7.4 - - + -
994A THR 4.0 0.2 - - - +
995A TYR* 2.8 49.0 + - + +
997A ASP* 1.3 77.2 - - - +
999A THR* 1.3 54.6 + - - +
1001A LEU* 3.3 3.0 + - - +
1002A LYS* 2.9 42.0 + - - +
1023A LEU* 3.5 22.1 - - + +
1027A VAL* 3.5 27.4 - - + -
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Residues in contact with THR 999 (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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995A TYR* 3.0 23.8 + - - -
996A HIS* 3.1 21.7 + - + +
998A VAL* 1.3 77.4 - - - +
1000A ARG* 1.3 62.1 + - - +
1002A LYS* 3.2 13.8 + - + +
1003A ARG* 3.0 22.2 + - + +
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Residues in contact with ARG1000 (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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869A LYS* 4.5 3.2 - - - +
896A LEU* 3.3 34.3 - - + +
897A SER* 3.9 10.5 + - - -
900A GLU* 2.3 38.1 + - - +
965A SER* 3.8 7.3 + - - -
996A HIS* 2.9 43.5 + - + +
997A ASP* 2.9 33.6 + - - +
999A THR* 1.3 74.4 - - + +
1001A LEU* 1.3 58.5 + - - +
1003A ARG* 3.2 10.8 + - - +
1004A LEU* 2.9 28.9 + - - +
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Residues in contact with LEU1001 (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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896A LEU* 3.6 23.6 - - + -
966A LEU* 3.2 38.1 - - + +
967A PRO* 3.5 20.2 - - + +
968A LYS* 3.6 26.7 - - + -
997A ASP 2.9 16.3 + - - +
998A VAL 3.7 1.1 - - - +
1000A ARG* 1.3 73.6 - - - +
1002A LYS* 1.3 60.4 + - - +
1004A LEU* 3.2 18.0 + - + +
1005A ILE* 2.9 33.3 + - - +
1023A LEU* 3.6 21.5 - - + -
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Residues in contact with LYS1002 (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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995A TYR* 4.2 14.8 + - - -
998A VAL* 2.9 33.2 + - - +
999A THR* 3.2 15.5 + - + +
1001A LEU* 1.3 73.5 - - - +
1003A ARG* 1.3 64.5 + - - +
1005A ILE* 3.2 4.2 + - - +
1006A MET* 3.0 38.5 + - + +
1020A PHE* 3.6 33.0 - - + -
1023A LEU* 3.9 10.1 - - + -
1024A TYR* 6.2 4.0 - - - -
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Residues in contact with ARG1003 (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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999A THR* 3.0 13.3 + - + +
1000A ARG* 3.2 12.8 + - - +
1002A LYS* 1.3 76.4 - - - +
1004A LEU* 1.3 64.0 + - + +
1006A MET* 3.3 11.7 + - - +
1007A MET* 3.1 65.1 + - - +
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Residues in contact with LEU1004 (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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896A LEU* 3.6 35.9 - - + +
968A LYS* 5.3 10.1 - - + -
1000A ARG 2.9 13.5 + - - +
1001A LEU* 3.2 25.5 + - + +
1003A ARG* 1.3 77.4 - - + +
1005A ILE* 1.3 63.6 + - + +
1007A MET* 3.4 28.8 + - + +
1008A GLU* 3.9 10.4 - - - +
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Residues in contact with ILE1005 (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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968A LYS* 5.0 18.6 - - + +
1001A LEU* 2.9 21.2 + - + +
1002A LYS 3.2 4.9 + - - +
1004A LEU* 1.3 77.2 - - - +
1006A MET* 1.3 57.9 + - - +
1008A GLU* 2.8 31.1 - - + +
1016A ARG* 4.0 13.5 + - + +
1019A HIS* 3.8 48.2 - - + +
1020A PHE* 4.0 28.0 - - + -
1023A LEU* 3.7 25.8 - - + -
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Residues in contact with MET1006 (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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1002A LYS* 3.0 30.9 + - + +
1003A ARG* 3.3 12.6 + - - +
1005A ILE* 1.3 74.1 - - - +
1007A MET* 1.3 56.7 + - - +
1008A GLU 3.2 8.6 + - - -
1016A ARG* 4.1 26.2 + - - +
1020A PHE* 3.8 28.3 - - + -
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Residues in contact with MET1007 (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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1003A ARG* 3.1 61.1 + - - +
1004A LEU* 3.4 22.8 + - + +
1005A ILE 3.3 1.2 - - - -
1006A MET* 1.3 76.2 - - - +
1008A GLU* 1.3 62.8 + - - +
1009A LYS 3.9 2.0 + - - -
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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