Contacts of the helix formed by residues 1015 - 1029 (chain A) in PDB entry 6AGF
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 LYS1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A GLY* 1.3 78.8 - - - +
1016A LYS* 1.3 62.8 + - + +
1017A TRP 3.6 0.2 + - - -
1018A TRP* 3.9 6.3 + - - +
1019A THR* 3.7 16.1 + - - +
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Residues in contact with LYS1016 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A GLY* 4.7 13.7 - - - +
1015A LYS* 1.3 80.6 - - + +
1017A TRP* 1.3 65.4 + - - +
1019A THR* 2.8 25.8 - - + +
1020A LEU* 3.2 9.9 + - - +
182B TYR* 3.3 22.9 + - - +
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Residues in contact with TRP1017 (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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1014A GLY* 3.5 17.1 + - - +
1015A LYS 3.4 0.6 - - - -
1016A LYS* 1.3 82.1 - - - +
1018A TRP* 1.3 71.4 + + + +
1020A LEU* 3.1 26.9 + - + +
1021A ARG* 3.0 62.3 + - - +
1085A VAL* 5.1 16.8 - - + -
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Residues in contact with TRP1018 (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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1014A GLY 4.1 5.3 + - - +
1015A LYS 3.9 8.7 + - - +
1016A LYS 3.3 0.2 - - - -
1017A TRP* 1.3 89.2 - + + +
1019A THR* 1.3 64.1 + - - +
1021A ARG* 3.2 29.9 + - + +
1022A ARG* 2.8 61.5 + - + +
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Residues in contact with THR1019 (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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1015A LYS 3.7 6.0 + - - +
1016A LYS* 2.8 40.6 - - - +
1018A TRP* 1.3 79.5 - - - +
1020A LEU* 1.3 57.0 + - - +
1022A ARG* 3.2 13.3 + - - +
1023A ALA* 2.9 28.4 + - - +
182B TYR* 3.2 29.6 + - + +
185B ILE* 4.0 20.6 - - - +
186B ALA* 4.6 9.0 + - + +
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Residues in contact with LEU1020 (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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1016A LYS 3.5 9.9 - - - +
1017A TRP* 3.1 33.1 + - + +
1019A THR* 1.3 82.7 - - - +
1021A ARG* 1.3 61.4 + - - +
1023A ALA* 3.2 5.3 + - + +
1024A CYS* 2.9 36.0 + - - +
1085A VAL* 4.7 9.4 - - + -
178B MET* 4.7 18.2 - - + -
182B TYR* 3.8 19.1 - - + -
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Residues in contact with ARG1021 (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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1017A TRP* 3.0 48.5 + - + +
1018A TRP* 3.2 31.8 + - + +
1020A LEU* 1.3 80.0 - - - +
1022A ARG* 1.3 62.4 + - - +
1024A CYS* 3.2 5.3 + - - +
1025A PHE* 3.1 22.9 + - - +
1084A TRP 4.4 4.0 + - - -
1085A VAL* 2.7 38.4 + - + +
1086A ALA* 4.4 7.7 + - - +
1087A TYR 4.1 4.0 + - - -
1088A GLY* 3.2 29.0 - - - +
1089A PHE* 4.5 5.3 - - - +
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Residues in contact with ARG1022 (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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1018A TRP* 2.8 62.3 + - + +
1019A THR* 3.5 9.3 + - - +
1021A ARG* 1.3 76.8 - - - +
1023A ALA* 1.3 63.0 + - - +
1025A PHE* 3.5 19.2 + - - +
1026A LYS* 3.6 12.0 + - - +
185B ILE* 3.3 38.8 - - + +
189B THR* 4.6 8.7 + - - -
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Residues in contact with ALA1023 (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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1019A THR 2.9 13.5 + - - +
1020A LEU* 3.3 13.5 - - + +
1022A ARG* 1.3 75.9 - - - +
1024A CYS* 1.3 65.1 + - - +
1026A LYS* 3.3 14.5 + - - +
1027A ILE* 3.7 13.2 + - - +
178B MET* 4.7 4.3 - - + +
181B CYS* 4.1 12.3 - - + +
182B TYR* 4.0 33.0 - - + +
185B ILE* 4.4 10.3 - - + +
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Residues in contact with CYS1024 (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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1020A LEU* 2.9 22.7 + - - +
1021A ARG 3.7 7.0 - - - +
1023A ALA* 1.3 76.0 - - - +
1025A PHE* 1.3 56.4 + - - +
1027A ILE* 2.7 37.9 + - - +
1028A VAL* 3.3 8.1 + - - +
1082A LEU* 3.5 32.3 - - + +
1085A VAL* 4.0 19.1 - - + -
1086A ALA* 3.9 18.6 - - + +
178B MET* 4.6 14.4 - - - -
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Residues in contact with PHE1025 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A ARG 3.1 10.5 + - - +
1022A ARG* 3.5 14.1 - - - +
1024A CYS* 1.3 79.7 - - - +
1026A LYS* 1.3 64.8 + - + +
1028A VAL* 3.5 2.2 + - - +
1029A GLU* 3.3 43.1 + - + +
1086A ALA* 3.7 26.4 - - - +
1087A TYR* 3.8 31.0 - + - -
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Residues in contact with LYS1026 (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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1022A ARG* 3.6 7.5 + - - +
1023A ALA 3.3 10.9 + - - +
1024A CYS 3.0 1.8 - - - -
1025A PHE* 1.3 81.9 - - + +
1027A ILE* 1.3 63.9 + - - +
1029A GLU* 4.2 4.5 - - + +
1030A HIS* 3.3 26.5 + - + +
181B CYS* 5.1 15.7 - - + -
184B LYS* 6.1 4.0 - - + -
185B ILE* 3.9 30.1 - - + -
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Residues in contact with ILE1027 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023A ALA 4.1 11.2 - - - +
1024A CYS* 2.7 23.5 + - - +
1026A LYS* 1.3 72.3 - - - +
1028A VAL* 1.3 64.3 + - - +
1030A HIS* 3.2 18.6 + - - +
1033A PHE* 3.3 29.6 - - + +
1082A LEU* 4.0 22.4 - - + -
174B LEU* 5.0 11.9 - - + +
177B GLU* 3.9 30.5 - - + +
178B MET* 4.0 19.7 - - + +
181B CYS* 4.4 13.5 - - + -
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Residues in contact with VAL1028 (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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1024A CYS 3.3 2.1 + - - +
1025A PHE 3.5 5.1 + - - +
1026A LYS 3.5 0.2 - - - -
1027A ILE* 1.3 76.1 - - - +
1029A GLU* 1.3 61.7 + - - +
1030A HIS 3.3 5.2 + - - +
1033A PHE* 3.9 21.4 - - + -
1034A GLU* 5.0 7.3 + - - +
1082A LEU* 3.7 32.1 - - + +
1083A LYS* 3.2 33.4 - - + +
1086A ALA* 3.8 22.7 - - + -
1087A TYR* 3.5 26.0 - - + +
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Residues in contact with GLU1029 (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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1025A PHE* 3.3 36.5 + - + +
1026A LYS* 4.6 5.6 - - + +
1028A VAL* 1.3 79.9 - - - +
1030A HIS* 1.3 62.6 + - - +
1031A ASN* 3.8 1.6 + - - +
1034A GLU* 5.7 1.1 - - - +
1087A TYR* 4.7 11.5 + - + -
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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