Contacts of the helix formed by residues 1104 - 1121 (chain r) in PDB entry 6FF7
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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007r PRO* 4.1 31.9 - - + +
1099r VAL* 3.3 13.7 + - + +
1102r ARG* 3.6 6.0 - - + -
1103r GLY* 1.3 73.6 - - - +
1105r ALA* 1.3 65.3 + - - +
1106r GLN 3.5 1.3 - - - -
1107r LEU* 3.4 9.2 + - + -
1108r THR* 3.2 21.8 + - - -
1231r GLU 4.1 4.3 - - - -
1232r VAL* 5.4 0.2 - - - +
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Residues in contact with ALA1105 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103r GLY 3.3 4.8 + - - -
1104r TRP* 1.3 69.9 - - - +
1106r GLN* 1.3 66.0 + - - +
1108r THR* 3.0 8.7 + - - -
1109r ASP* 3.0 21.8 + - - +
1226r GLU* 4.9 7.6 - - + -
1230r SER* 4.1 6.1 - - - +
1231r GLU 3.0 34.9 + - - +
1232r VAL 4.2 10.5 - - - +
1233r ILE* 4.3 7.9 - - + +
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Residues in contact with GLN1106 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007r PRO 5.0 7.4 - - - +
1104r TRP 3.5 0.4 - - - -
1105r ALA* 1.3 78.2 - - - +
1107r LEU* 1.3 57.5 + - - +
1109r ASP* 3.2 10.1 + - - +
1110r LYS* 3.0 26.1 + - - +
1230r SER 4.6 10.2 + - - +
1231r GLU* 4.3 3.6 + - - +
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Residues in contact with LEU1107 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006r LYS 5.0 4.7 - - - +
1007r PRO* 4.1 19.6 + - + +
1009r LEU* 4.8 14.1 - - + +
1099r VAL* 4.9 11.9 - - + +
1104r TRP* 3.4 11.9 + - + +
1105r ALA 3.2 0.6 - - - -
1106r GLN* 1.3 76.2 - - - +
1108r THR* 1.3 62.3 + - - +
1110r LYS* 3.9 7.4 - - - +
1111r THR* 2.9 30.5 + - - -
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Residues in contact with THR1108 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096r PHE* 4.9 4.6 - - - +
1099r VAL* 4.5 4.6 - - - +
1100r LEU* 4.2 32.5 - - - -
1103r GLY 6.3 0.2 - - - -
1104r TRP 3.2 12.4 + - - -
1105r ALA* 3.0 9.6 + - - -
1107r LEU* 1.3 73.6 - - - +
1109r ASP* 1.3 61.9 + - - +
1111r THR* 4.5 4.3 - - - +
1112r LEU* 3.0 31.7 + - - +
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Residues in contact with ASP1109 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105r ALA 3.0 11.9 + - - +
1106r GLN* 3.2 11.4 + - - +
1108r THR* 1.3 75.5 - - - +
1110r LYS* 1.3 66.8 + - - +
1111r THR 3.0 0.5 + - - -
1112r LEU* 3.9 2.7 - - - +
1113r ASN* 2.9 27.0 + - - +
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Residues in contact with LYS1110 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009r LEU 5.5 4.9 - - - +
1010r SER 6.0 0.2 - - - -
1011r GLU* 5.5 15.7 - - + +
1014r LEU* 5.8 6.3 - - + -
1106r GLN 3.0 16.2 + - - +
1107r LEU* 3.4 8.0 + - - +
1109r ASP* 1.3 75.0 - - - +
1111r THR* 1.3 57.3 + - - +
1113r ASN* 3.9 5.0 - - - +
1114r LEU* 3.0 28.1 + - - +
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Residues in contact with THR1111 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092r MET* 4.6 7.7 - - - +
1095r ILE* 4.8 6.3 - - - -
1096r PHE* 4.0 31.1 - - - +
1099r VAL* 5.6 2.5 - - - -
1107r LEU 2.9 18.7 + - - -
1108r THR* 4.2 1.3 - - - -
1110r LYS* 1.3 74.4 - - - +
1112r LEU* 1.3 65.5 + - - +
1113r ASN 3.2 0.9 - - - -
1114r LEU* 3.4 7.0 + - - +
1115r CYS* 3.0 22.0 + - - +
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Residues in contact with LEU1112 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096r PHE* 4.4 9.7 - - + +
1108r THR 3.0 18.6 + - - +
1109r ASP* 4.1 2.9 - - - +
1111r THR* 1.3 76.1 - - - +
1113r ASN* 1.3 64.4 + - - +
1115r CYS* 3.1 10.0 + - - +
1116r LYS* 2.9 22.6 + - - +
1273r ASP 5.4 5.2 - - - +
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Residues in contact with ASN1113 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109r ASP 2.9 17.3 + - - +
1110r LYS* 3.9 5.4 - - - +
1112r LEU* 1.3 75.2 - - - +
1114r LEU* 1.3 64.4 + - - +
1116r LYS* 3.3 8.2 + - - +
1117r MET* 2.9 23.1 + - - +
1124r GLN* 6.3 3.4 - - + -
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Residues in contact with LEU1114 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092r MET* 5.3 9.0 - - + -
1110r LYS 3.0 19.7 + - - +
1111r THR* 3.6 7.9 - - - +
1112r LEU 3.3 0.2 - - - -
1113r ASN* 1.3 75.9 - - - +
1115r CYS* 1.3 63.4 + - - +
1117r MET* 2.8 18.8 + - - +
1118r ILE* 2.9 14.2 + - - +
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Residues in contact with CYS1115 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089r GLY* 5.8 2.7 - - - +
1092r MET* 4.7 14.6 - - + +
1093r ARG* 5.3 11.4 - - + +
1096r PHE* 5.8 2.2 - - + -
1111r THR 3.0 13.8 + - - +
1112r LEU* 3.2 12.8 - - - +
1114r LEU* 1.3 76.0 - - - +
1116r LYS* 1.3 58.5 + - - +
1118r ILE* 3.2 7.0 + - - +
1119r ASP* 2.9 29.0 + - - +
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Residues in contact with LYS1116 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112r LEU 2.9 12.6 + - - +
1113r ASN* 3.6 10.3 - - - +
1115r CYS* 1.3 76.7 - - - +
1117r MET* 1.3 58.0 + - - +
1119r ASP* 3.3 6.4 + - - +
1120r LYS* 2.9 34.5 + - - +
1273r ASP 4.8 8.3 - - - +
1274r ARG* 4.1 19.0 - - - +
1275r TRP 4.9 1.3 - - - +
1276r LEU* 4.2 22.9 - - + -
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Residues in contact with MET1117 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067r ILE* 4.4 13.7 - - + +
1113r ASN 2.9 12.7 + - - +
1114r LEU* 2.8 13.5 + - - +
1116r LYS* 1.3 78.1 - - - +
1118r ILE* 1.3 57.0 + - - +
1120r LYS* 5.1 0.7 - - - -
1121r ARG* 3.0 22.2 + - - -
1122r MET 3.1 31.8 + - - +
1123r TRP* 4.8 5.6 - - - -
1124r GLN 5.5 1.3 - - - +
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Residues in contact with ILE1118 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067r ILE* 5.6 4.7 - - - +
1085r THR 5.7 2.2 - - - +
1088r ALA* 5.4 14.1 - - + +
1089r GLY* 5.4 9.6 - - - -
1114r LEU 2.9 10.6 + - - +
1115r CYS* 3.5 10.8 - - - +
1117r MET* 1.3 75.5 - - - +
1119r ASP* 1.3 67.7 + - - +
1121r ARG* 3.3 12.5 + - - +
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Residues in contact with ASP1119 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115r CYS 2.9 17.5 + - - +
1116r LYS* 3.3 8.5 + - - +
1118r ILE* 1.3 78.1 - - - +
1120r LYS* 1.3 58.5 + - + +
1121r ARG* 5.0 1.0 - - - +
1274r ARG* 5.5 6.1 - - + +
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Residues in contact with LYS1120 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116r LYS 2.9 18.7 + - - +
1117r MET* 5.1 0.9 - - - -
1119r ASP* 1.3 73.8 - - + +
1121r ARG* 1.3 71.5 + - - +
1122r MET* 4.5 10.2 - - + +
1131r GLN* 5.5 11.7 - - + -
1274r ARG 6.0 1.8 - - - +
1276r LEU* 5.1 13.2 - - + -
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Residues in contact with ARG1121 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066r PHE 4.5 10.8 - - - +
1067r ILE* 3.4 17.2 - - - +
1069r GLN* 4.9 9.2 - - + +
1117r MET 3.0 11.7 + - - -
1118r ILE* 3.3 9.6 + - - +
1119r ASP 5.0 0.9 - - - +
1120r LYS* 1.3 82.6 - - - +
1122r MET* 1.3 61.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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