Contacts of the helix formed by residues 1075 - 1088 (chain A) in PDB entry 6O0Z
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 ASP1075 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062A LEU* 6.0 0.9 - - - +
1063A ILE* 4.1 36.0 - - + +
1072A ILE* 5.6 3.9 - - + +
1073A VAL 3.8 1.6 - - - -
1074A TRP* 1.3 70.2 - - - +
1076A LYS* 1.3 68.8 + - - +
1077A GLY 4.3 4.3 + - - -
1078A ARG* 3.4 33.5 + - + +
1079A ASP* 3.0 34.4 + - - +
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Residues in contact with LYS1076 (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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1045A PHE 4.4 7.6 + - - -
1046A PHE 3.7 17.5 - - - +
1047A LYS 4.4 1.4 + - - -
1048A THR* 3.5 33.6 - - - +
1060A ARG* 5.1 1.0 + - - +
1061A PRO 3.5 21.4 + - - -
1062A LEU* 3.3 40.1 + - + +
1064A GLU* 4.3 3.5 + - - -
1074A TRP* 3.5 34.5 - - + +
1075A ASP* 1.3 76.3 + - - +
1077A GLY* 1.3 59.8 + - - +
1079A ASP* 4.0 1.1 - - - +
1080A PHE* 3.0 48.9 + - + +
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Residues in contact with GLY1077 (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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1062A LEU* 5.5 1.0 - - - +
1075A ASP* 4.3 3.0 + - - -
1076A LYS* 1.3 79.0 - - - +
1078A ARG* 1.3 57.9 + - - +
1080A PHE* 3.9 3.7 - - - +
1081A ALA* 2.9 31.6 + - - +
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Residues in contact with ARG1078 (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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24A GLU* 5.6 8.1 + - - -
26A LYS* 6.2 0.4 - - - +
1075A ASP* 3.4 31.7 + - + +
1076A LYS 3.4 0.2 - - - -
1077A GLY* 1.3 74.6 - - - +
1079A ASP* 1.3 66.1 + - - +
1081A ALA* 3.4 6.0 + - - +
1082A THR* 2.8 33.5 + - - +
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Residues in contact with ASP1079 (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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24A GLU 5.0 3.8 - - - +
25A TYR* 3.3 26.7 - - + +
1073A VAL 3.4 7.6 - - - +
1074A TRP* 3.2 42.8 - - + -
1075A ASP* 3.0 24.5 + - - +
1076A LYS 4.3 1.1 - - - +
1078A ARG* 1.3 79.2 - - - +
1080A PHE* 1.3 63.8 + - - +
1082A THR* 3.3 7.2 + - - -
1083A VAL* 2.9 33.8 + - + +
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Residues in contact with PHE1080 (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 PHE* 4.6 9.4 - + - -
970A PHE* 3.5 48.2 - + + -
972A PHE* 4.6 14.8 - + - -
1046A PHE 4.7 0.4 - - - -
1074A TRP* 3.5 33.7 - + - -
1076A LYS* 3.0 35.9 + - + +
1077A GLY* 4.1 3.8 - - - +
1079A ASP* 1.3 77.7 - - - +
1081A ALA* 1.3 58.9 + - - +
1083A VAL* 3.3 4.7 + - + +
1084A ARG* 3.0 54.3 + - - +
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Residues in contact with ALA1081 (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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1077A GLY 2.9 19.0 + - - +
1078A ARG* 3.7 5.8 - - - +
1080A PHE* 1.3 75.4 - - - +
1082A THR* 1.3 58.5 + - - +
1084A ARG* 3.5 8.6 + - - +
1085A LYS* 2.9 30.0 + - - +
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Residues in contact with THR1082 (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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24A GLU 4.3 5.0 + - - +
25A TYR* 3.3 29.2 - - + +
26A LYS* 3.8 28.2 - - + +
988A TYR* 4.6 0.4 - - - +
1078A ARG* 2.8 23.6 + - - +
1079A ASP* 3.6 8.2 + - - -
1080A PHE 3.2 0.2 - - - -
1081A ALA* 1.3 77.3 - - - +
1083A VAL* 1.3 56.3 + - - +
1085A LYS* 3.3 6.6 + - + +
1086A VAL* 2.9 32.9 + - + +
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Residues in contact with VAL1083 (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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25A TYR* 5.6 3.6 - - + -
966A PHE* 5.3 3.1 - - + -
972A PHE* 3.6 37.2 - - + -
988A TYR* 3.7 24.9 - - + +
989A LEU* 4.7 6.3 - - + -
992A VAL* 5.2 14.6 - - + -
1074A TRP* 5.2 9.6 - - + -
1079A ASP* 2.9 21.7 + - + +
1080A PHE* 3.3 6.9 + - + +
1082A THR* 1.3 74.2 - - - +
1084A ARG* 1.3 59.0 + - - +
1087A LEU* 2.9 42.7 + - + +
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Residues in contact with ARG1084 (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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970A PHE* 4.7 10.3 + - - +
971A GLN* 5.2 6.3 + - - -
972A PHE* 3.3 31.7 - - + -
1080A PHE* 3.0 45.1 + - - +
1081A ALA* 3.8 7.6 - - - +
1083A VAL* 1.3 77.2 - - - +
1085A LYS* 1.3 55.7 + - - +
1087A LEU* 3.7 4.2 - - - +
1088A SER* 3.0 35.4 + - - +
1230A SER* 5.9 2.7 - - - +
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Residues in contact with LYS1085 (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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1081A ALA 2.9 18.7 + - - +
1082A THR* 3.3 7.6 + - + +
1084A ARG* 1.3 76.7 - - - +
1086A VAL* 1.3 64.5 + - + +
1088A SER* 3.7 4.8 + - - -
1089A MET* 3.6 24.4 + - - +
87B G 5.7 4.3 + - - -
88B A 4.5 37.0 + - - +
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Residues in contact with VAL1086 (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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25A TYR 4.6 0.2 - - - +
26A LYS* 4.9 1.1 - - + -
27A VAL* 3.9 36.3 - - + +
48A ILE* 4.8 9.9 - - + +
985A HIS* 4.4 6.7 + - + -
988A TYR* 3.6 43.1 - - + +
1082A THR* 2.9 29.3 + - + +
1083A VAL 4.0 2.5 - - - +
1085A LYS* 1.3 78.9 - - + +
1087A LEU* 1.3 62.4 + - + +
1089A MET* 3.1 28.9 + - + +
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Residues in contact with LEU1087 (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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967A ARG* 4.9 8.1 - - - +
972A PHE* 5.4 13.9 - - + -
985A HIS* 3.5 57.4 - - + +
988A TYR* 3.9 28.5 - - + -
989A LEU* 4.6 17.5 - - + -
1083A VAL* 2.9 31.1 + - + +
1084A ARG* 3.9 5.4 - - - +
1086A VAL* 1.3 77.1 - - + +
1088A SER* 1.3 59.3 + - - +
1089A MET 3.4 1.8 + - - +
1230A SER* 5.6 2.7 - - - -
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Residues in contact with SER1088 (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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1084A ARG* 3.0 18.7 + - - +
1085A LYS* 3.9 6.7 - - - -
1086A VAL 3.2 0.4 - - - -
1087A LEU* 1.3 75.3 - - - +
1089A MET* 1.3 62.8 + - - +
1090A PRO* 3.6 6.9 - - - +
1229A PRO* 6.1 1.6 - - - -
1230A SER* 3.4 32.2 + - - +
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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