Contacts of the helix formed by residues 1104 - 1121 (chain D) in PDB entry 6AH0
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 TRP1104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007D PRO* 5.5 12.6 - - - -
1099D VAL 3.3 14.8 + - - +
1100D LEU* 5.1 0.4 - - - +
1102D ARG 3.6 1.4 - - - -
1103D GLY* 1.3 74.0 - - - +
1105D ALA* 1.3 65.3 + - - +
1106D GLN 3.5 1.6 - - - -
1107D LEU* 3.4 4.5 + - - -
1108D THR* 3.2 17.7 + - - -
1231D GLU 4.1 4.5 - - - -
1232D VAL* 5.4 0.2 - - - +
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Residues in contact with ALA1105 (chain D).
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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1103D GLY 3.3 6.5 + - - -
1104D TRP* 1.3 70.0 - - - +
1106D GLN* 1.3 64.2 + - - +
1108D THR* 3.0 4.2 + - - +
1109D ASP* 3.0 19.4 + - - -
1230D SER 5.2 2.5 - - - -
1231D GLU* 3.0 22.0 + - - +
1232D VAL 5.0 0.7 - - - -
1233D ILE* 4.8 6.3 - - - +
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Residues in contact with GLN1106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D PRO 5.7 0.7 - - - -
1104D TRP 3.5 0.4 - - - -
1105D ALA* 1.3 73.9 - - - +
1107D LEU* 1.3 57.2 + - - +
1109D ASP* 3.2 4.2 + - - +
1110D LYS* 3.0 23.0 + - - -
1230D SER 4.6 10.0 + - - -
1231D GLU* 4.3 4.2 + - - +
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Residues in contact with LEU1107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D PRO 4.6 13.6 + - - -
1009D LEU 5.2 8.7 - - - -
1096D PHE* 6.0 0.2 - - - -
1099D VAL* 6.1 1.3 - - - -
1104D TRP 3.4 5.6 + - - -
1105D ALA 3.2 0.6 - - - -
1106D GLN* 1.3 74.3 - - - +
1108D THR* 1.3 61.0 + - - +
1110D LYS* 3.8 2.3 - - - +
1111D THR* 2.9 25.1 + - - -
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Residues in contact with THR1108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096D PHE* 5.3 8.2 - - - +
1099D VAL* 5.2 12.8 + - - +
1100D LEU* 5.2 4.9 - - - +
1104D TRP 3.2 10.7 + - - -
1105D ALA* 3.0 7.7 + - - +
1107D LEU* 1.3 73.5 - - - +
1109D ASP* 1.3 61.0 + - - +
1111D THR* 4.5 1.1 - - - +
1112D LEU* 3.0 25.8 + - - -
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Residues in contact with ASP1109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105D ALA 3.0 13.3 + - - -
1106D GLN* 3.2 4.2 + - - +
1108D THR* 1.3 74.6 - - - +
1110D LYS* 1.3 65.5 + - - +
1111D THR 3.0 0.5 + - - -
1112D LEU* 3.9 0.2 - - - -
1113D ASN* 2.9 22.9 + - - -
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Residues in contact with LYS1110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106D GLN 3.0 13.5 + - - -
1107D LEU* 3.4 4.0 + - - +
1109D ASP* 1.3 73.3 - - - +
1111D THR* 1.3 56.9 + - - +
1113D ASN* 3.9 0.7 - - - +
1114D LEU* 3.0 23.6 + - - -
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Residues in contact with THR1111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092D MET* 4.8 9.4 - - - +
1096D PHE* 5.2 13.2 - - - +
1107D LEU 2.9 17.1 + - - -
1108D THR* 4.0 1.1 - - - +
1110D LYS* 1.3 74.4 - - - +
1112D LEU* 1.3 66.4 + - - +
1113D ASN 3.2 1.1 - - - -
1114D LEU* 3.4 1.4 + - - +
1115D CYS* 3.0 19.4 + - - -
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Residues in contact with LEU1112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096D PHE* 5.3 3.2 - - - +
1108D THR 3.0 16.8 + - - -
1109D ASP* 3.9 0.4 - - - +
1111D THR* 1.3 76.2 - - - +
1113D ASN* 1.3 62.5 + - - +
1115D CYS* 3.1 4.1 + - - +
1116D LYS* 2.9 19.6 + - - -
1273D ASP 5.4 3.5 - - - +
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Residues in contact with ASN1113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D ASP 2.9 15.3 + - - -
1110D LYS* 4.0 1.6 - - - +
1112D LEU* 1.3 73.9 - - - +
1114D LEU* 1.3 65.2 + - - +
1116D LYS* 3.3 3.2 + - - +
1117D MET* 2.9 19.8 + - - -
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Residues in contact with LEU1114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110D LYS 3.0 16.6 + - - -
1111D THR* 3.4 4.0 + - - +
1112D LEU 3.3 0.2 - - - -
1113D ASN* 1.3 75.2 - - - +
1115D CYS* 1.3 62.7 + - - +
1117D MET* 2.8 13.2 + - - +
1118D ILE* 2.9 11.8 + - - -
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Residues in contact with CYS1115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D GLY* 6.1 2.5 - - - -
1092D MET* 5.9 9.1 - - - +
1111D THR 3.0 14.6 + - - -
1112D LEU* 3.1 5.3 + - - +
1114D LEU* 1.3 74.1 - - - +
1116D LYS* 1.3 56.3 + - - +
1118D ILE* 3.2 1.7 + - - +
1119D ASP* 2.9 26.0 + - - -
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Residues in contact with LYS1116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112D LEU 2.9 12.9 + - - -
1113D ASN* 3.7 3.8 - - - +
1114D LEU 3.2 0.2 - - - -
1115D CYS* 1.3 75.5 - - - +
1117D MET* 1.3 57.9 + - - +
1119D ASP* 3.7 1.5 - - - +
1120D LYS* 2.9 28.1 + - - -
1273D ASP 5.4 4.2 + - - -
1274D ARG* 4.6 15.6 - - - +
1275D TRP 6.1 0.2 - - - -
1276D LEU* 5.7 8.5 - - - +
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Residues in contact with MET1117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067D ILE* 4.8 5.9 - - - -
1113D ASN 2.9 11.2 + - - -
1114D LEU* 2.8 8.2 + - - +
1116D LYS* 1.3 76.7 - - - +
1118D ILE* 1.3 57.6 + - - +
1121D ARG* 3.0 22.3 + - - -
1122D MET 3.2 28.8 + - - +
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Residues in contact with ILE1118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067D ILE* 6.0 2.7 - - - +
1114D LEU 2.9 11.3 + - - -
1115D CYS* 3.7 3.4 - - - +
1117D MET* 1.3 76.0 - - - +
1119D ASP* 1.3 65.5 + - - +
1121D ARG* 3.3 11.1 + - - -
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Residues in contact with ASP1119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115D CYS 2.9 14.3 + - - -
1116D LYS* 3.7 3.8 - - - +
1118D ILE* 1.3 75.8 - - - +
1120D LYS* 1.3 58.2 + - - +
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Residues in contact with LYS1120 (chain D).
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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1116D LYS 2.9 17.8 + - - -
1117D MET* 5.3 0.2 - - - +
1119D ASP* 1.3 72.2 - - - +
1121D ARG* 1.3 66.2 + - - +
1122D MET* 3.4 2.2 - - - -
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Residues in contact with ARG1121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066D PHE 4.8 4.8 - - - +
1067D ILE* 3.5 20.7 - - - +
1069D GLN* 5.4 1.7 + - - -
1117D MET 3.0 11.0 + - - -
1118D ILE* 3.3 9.0 + - - +
1119D ASP 3.7 0.2 + - - -
1120D LYS* 1.3 81.0 - - - +
1122D MET* 1.3 57.7 + - - +
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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