Contacts of the helix formed by residues 1109 - 1122 (chain u) 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 ARG1109 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392Z U 5.8 3.8 - - - +
1100u ASN 4.1 13.5 - - - +
1101u LEU* 4.9 12.9 - - + +
1103u VAL* 5.1 5.8 - - + +
1105u GLU 4.0 13.1 + - - +
1106u ARG* 5.5 1.8 - - - -
1107u GLN 4.5 0.6 - - - +
1108u ASN* 1.3 78.5 - - - +
1110u VAL* 1.3 59.3 + - - +
1111u CYS 3.4 0.2 - - - -
1112u THR* 4.0 2.5 - - - +
1113u THR* 3.2 21.8 + - - -
1142u ASN* 5.8 7.9 - - + +
1146u GLY* 5.2 8.2 - - - -
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Residues in contact with VAL1110 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393Z G 4.9 14.4 - - - +
394Z A 4.5 28.6 - - - +
395Z C 5.7 1.8 - - - +
1106u ARG* 5.7 1.7 - - + +
1107u GLN* 5.0 9.5 - - - +
1108u ASN 4.3 1.6 - - - +
1109u ARG* 1.3 77.2 - - - +
1111u CYS* 1.3 60.1 + - - +
1112u THR 3.2 0.4 - - - -
1113u THR* 3.2 9.5 + - - -
1114u VAL* 3.0 28.1 + - - +
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Residues in contact with CYS1111 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Z A 5.6 6.7 - - + +
1066u LEU* 4.9 11.0 - - + -
1074u ARG* 5.1 20.6 - - + +
1078u VAL* 4.8 5.0 - - - +
1107u GLN* 3.7 24.4 - - - +
1108u ASN* 4.2 4.4 - - - +
1109u ARG 3.4 1.0 - - - +
1110u VAL* 1.3 79.5 - - - +
1112u THR* 1.3 55.5 + - - +
1114u VAL* 4.2 8.0 - - - +
1115u ALA* 3.7 14.6 + - - +
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Residues in contact with THR1112 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097u LEU* 4.2 16.4 - - - +
1100u ASN* 3.9 26.0 - - - -
1108u ASN 3.8 18.3 + - - -
1109u ARG 3.9 3.3 + - - -
1110u VAL 3.2 0.2 - - - -
1111u CYS* 1.3 76.2 - - - +
1113u THR* 1.3 57.2 + - - +
1114u VAL 3.3 1.3 - - - -
1115u ALA* 3.2 11.7 + - - +
1116u ILE* 2.9 27.0 + - - +
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Residues in contact with THR1113 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109u ARG 3.2 17.7 + - - -
1110u VAL* 3.3 14.4 - - - -
1112u THR* 1.3 73.9 - - - +
1114u VAL* 1.3 59.0 + - - +
1116u ILE* 3.2 9.9 + - - +
1117u ALA* 3.0 24.9 + - - +
1146u GLY* 4.4 17.7 - - - -
1149u LYS* 4.8 10.8 - - - -
1150u SER* 4.1 16.4 - - - -
1153u PHE* 4.9 2.6 - - - +
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Residues in contact with VAL1114 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Z A 4.3 35.4 - - + +
1078u VAL* 4.3 9.8 - - + +
1110u VAL 3.0 14.9 + - - +
1111u CYS* 4.3 7.4 - - - +
1113u THR* 1.3 75.6 - - - +
1115u ALA* 1.3 57.2 + - - +
1117u ALA* 3.1 10.8 + - - +
1118u ILE* 2.9 27.9 + - - +
1153u PHE* 5.2 4.5 - - + -
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Residues in contact with ALA1115 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078u VAL* 4.1 13.9 - - + +
1081u PHE* 4.3 23.0 - - + +
1097u LEU* 5.1 9.0 - - + -
1111u CYS 3.7 7.3 + - - +
1112u THR* 3.2 22.4 + - - +
1113u THR 3.2 0.4 - - - -
1114u VAL* 1.3 75.9 - - - +
1116u ILE* 1.3 58.3 + - - +
1118u ILE* 3.3 3.3 + - - +
1119u VAL* 2.9 30.0 + - - +
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Residues in contact with ILE1116 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097u LEU* 5.2 10.7 - - + +
1112u THR 2.9 13.0 + - - +
1113u THR* 3.2 9.8 + - - +
1115u ALA* 1.3 73.3 - - - +
1117u ALA* 1.3 58.6 + - - +
1119u VAL* 3.6 5.2 + - - +
1120u ALA* 3.0 28.4 + - - +
1128u VAL* 5.2 4.6 - - + +
1150u SER* 4.0 18.6 - - - -
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Residues in contact with ALA1117 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113u THR 3.0 9.5 + - - +
1114u VAL* 3.1 10.5 + - - +
1116u ILE* 1.3 77.7 - - - +
1118u ILE* 1.3 56.9 + - - +
1120u ALA* 3.2 8.5 + - - +
1121u GLU* 2.9 30.0 + - - +
1150u SER 4.7 4.6 + - - +
1153u PHE* 3.6 41.3 - - + +
1154u LEU* 4.2 5.0 - - - +
1157u TYR* 5.1 5.3 - - + +
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Residues in contact with ILE1118 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078u VAL* 3.6 30.3 - - + +
1079u ASN* 5.2 2.2 - - - -
1082u GLY* 4.5 6.3 - - - -
1114u VAL 2.9 14.6 + - - +
1115u ALA* 3.3 4.4 + - - +
1117u ALA* 1.3 74.7 - - - +
1119u VAL* 1.3 62.6 + - - +
1121u GLU* 4.3 3.8 - - - +
1122u THR* 2.9 35.0 + - - -
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Residues in contact with VAL1119 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081u PHE* 5.3 2.7 - - + +
1082u GLY* 4.7 9.3 - - - -
1085u ALA* 4.4 19.9 - - + +
1090u PRO* 5.0 13.3 - - + +
1094u LEU* 6.5 1.1 - - + -
1115u ALA 2.9 16.7 + - - +
1116u ILE* 4.2 5.2 - - - +
1118u ILE* 1.3 76.7 - - - +
1120u ALA* 1.3 61.5 + - - +
1122u THR* 5.3 1.1 - - - -
1123u CYS* 4.1 17.0 + - - +
1124u SER 4.8 2.3 - - - +
1128u VAL* 5.2 9.3 - - + +
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Residues in contact with ALA1120 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116u ILE 3.0 19.7 + - - +
1117u ALA* 3.3 9.2 - - - +
1118u ILE 3.1 0.2 - - - -
1119u VAL* 1.3 78.9 - - - +
1121u GLU* 1.3 57.2 + - + +
1123u CYS 3.1 13.7 - - - +
1124u SER 4.2 7.9 - - - +
1125u PRO* 4.3 10.0 - - + +
1128u VAL* 4.8 14.1 - - + +
1154u LEU* 4.9 15.0 - - + -
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Residues in contact with GLU1121 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117u ALA 2.9 16.2 + - - +
1118u ILE* 3.2 3.3 + - - +
1120u ALA* 1.3 79.3 - - + +
1122u THR* 1.3 66.2 + - - +
1123u CYS 3.6 2.5 - - - +
1154u LEU 6.0 0.2 - - - +
1157u TYR* 4.3 25.6 - - + +
1158u ILE* 5.5 4.9 - - + +
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Residues in contact with THR1122 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082u GLY* 4.2 24.5 - - - -
1086u LYS* 5.3 5.4 - - - -
1118u ILE* 2.9 18.5 + - - -
1119u VAL* 5.3 0.4 - - - -
1121u GLU* 1.3 79.4 - - - +
1123u CYS* 1.3 61.0 + - - +
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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