Contacts of the helix formed by residues 1072 - 1089 (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 ALA1072 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033u GLU* 5.8 7.0 - - + -
1070u LYS* 3.1 13.6 + - + +
1071u LYS* 1.3 78.6 - - - +
1073u ILE* 1.3 59.6 + - - +
1074u ARG 3.3 0.2 - - - -
1075u ARG* 3.4 3.2 + - - +
1076u ALA* 3.0 30.7 + - - +
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Residues in contact with ILE1073 (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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1029u GLU* 5.5 1.8 - - - +
1032u GLN* 5.2 8.7 - - + +
1033u GLU* 5.0 21.8 - - + +
1036u ILE* 5.7 3.3 - - - +
1065u LEU 5.4 4.7 - - - +
1068u ALA* 4.5 23.3 - - + +
1070u LYS* 4.8 8.3 - - + +
1071u LYS 4.5 0.8 - - - +
1072u ALA* 1.3 78.0 - - - +
1074u ARG* 1.3 57.6 + - - +
1076u ALA* 3.3 4.2 + - - +
1077u THR* 2.9 34.4 + - - -
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Residues in contact with ARG1074 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Z A 3.2 25.1 - - + +
1066u LEU* 6.3 3.8 - - + +
1068u ALA* 4.9 10.1 + - + +
1071u LYS* 4.0 15.7 - - - +
1072u ALA 3.3 0.6 - - - -
1073u ILE* 1.3 79.7 - - - +
1075u ARG* 1.3 58.3 + - - +
1077u THR* 4.3 5.0 - - - -
1078u VAL* 4.3 12.5 + - - +
1111u CYS* 5.1 18.4 - - + +
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Residues in contact with ARG1075 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Z A 3.5 25.9 + - + +
1071u LYS 3.4 20.3 + - - +
1072u ALA* 4.1 3.6 - - - +
1073u ILE 3.2 0.4 - - - -
1074u ARG* 1.3 77.9 - - - +
1076u ALA* 1.3 60.1 + - - +
1077u THR 3.5 0.4 - - - -
1078u VAL* 4.4 3.4 + - - +
1079u ASN* 4.3 11.8 + - - +
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Residues in contact with ALA1076 (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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1033u GLU 5.9 1.3 - - - +
1036u ILE* 5.2 19.1 - - + +
1037u ASP* 5.4 7.4 - - + +
1040u GLY* 6.0 0.5 - - - -
1072u ALA 3.0 17.3 + - - +
1073u ILE* 4.0 4.5 - - - +
1075u ARG* 1.3 78.6 - - - +
1077u THR* 1.3 60.0 + - - +
1078u VAL 3.3 0.4 - - - -
1079u ASN* 3.2 9.6 + - - +
1080u THR* 3.0 24.5 + - - -
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Residues in contact with THR1077 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036u ILE* 5.3 11.2 - - - +
1062u LEU* 5.4 16.2 - - - +
1065u LEU* 5.7 7.4 - - - -
1073u ILE 2.9 16.9 + - - -
1074u ARG* 4.3 5.1 - - - -
1075u ARG 3.5 0.2 - - - -
1076u ALA* 1.3 78.9 - - - +
1078u VAL* 1.3 56.3 + - - +
1080u THR* 3.2 9.7 + - - -
1081u PHE* 2.9 26.0 + - - +
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Residues in contact with VAL1078 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Z A 5.2 4.5 - - - +
1074u ARG 4.3 14.3 + - - +
1075u ARG 4.4 4.2 + - - +
1076u ALA 3.3 0.6 - - - -
1077u THR* 1.3 75.5 - - - +
1079u ASN* 1.3 60.4 + - - +
1081u PHE* 3.3 9.4 + - - +
1082u GLY 2.9 22.2 + - - -
1111u CYS 4.8 4.5 - - - +
1114u VAL* 4.3 13.9 - - + +
1115u ALA* 4.1 26.9 - - + +
1118u ILE* 3.6 15.2 - - + +
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Residues in contact with ASN1079 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040u GLY* 5.9 0.7 - - - -
1075u ARG 4.3 7.4 + - - +
1076u ALA* 3.2 14.7 + - - +
1078u VAL* 1.3 76.3 - - - +
1080u THR* 1.3 59.9 + - - +
1082u GLY* 3.2 2.7 + - - +
1083u TYR* 3.0 28.8 + - - +
1118u ILE* 5.2 3.6 - - - -
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Residues in contact with THR1080 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036u ILE* 4.9 8.3 - - - -
1039u VAL* 5.2 5.6 - - - -
1040u GLY* 4.6 24.1 - - - -
1043u ALA* 4.5 4.6 - - - +
1076u ALA 3.0 13.0 + - - -
1077u THR* 3.2 12.7 + - - -
1079u ASN* 1.3 76.9 - - - +
1081u PHE* 1.3 55.5 + - - +
1083u TYR* 3.4 4.2 + - - +
1084u ILE* 2.9 30.1 + - - +
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Residues in contact with PHE1081 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059u CYS* 6.4 2.2 - - + -
1077u THR 2.9 13.0 + - - +
1078u VAL 3.3 9.6 + - - +
1080u THR* 1.3 75.7 - - - +
1082u GLY* 1.3 57.7 + - - +
1084u ILE* 3.3 7.2 + - - +
1085u ALA* 3.0 30.0 + - - +
1093u VAL* 5.6 4.4 - - + +
1115u ALA* 4.3 24.0 - - + +
1119u VAL* 5.3 2.9 - - + +
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Residues in contact with GLY1082 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078u VAL 2.9 14.5 + - - -
1079u ASN* 3.2 4.2 + - - -
1081u PHE* 1.3 76.8 - - - +
1083u TYR* 1.3 56.2 + - - +
1085u ALA* 3.4 4.7 + - - +
1086u LYS* 2.9 26.7 + - - +
1118u ILE* 4.4 23.1 - - - +
1119u VAL* 4.7 2.9 - - - -
1122u THR* 4.2 15.7 - - - -
1123u CYS* 5.4 0.3 + - - +
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Residues in contact with TYR1083 (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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1040u GLY* 5.1 1.1 - - - +
1043u ALA* 3.4 40.3 - - + +
1044u ASP* 4.1 12.1 - - + +
1079u ASN 3.0 15.5 + - - +
1080u THR* 4.2 0.4 - - - +
1082u GLY* 1.3 73.7 - - - +
1084u ILE* 1.3 61.1 + - - +
1086u LYS* 3.4 9.9 + - + +
1087u ALA* 2.9 27.7 + - - +
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Residues in contact with ILE1084 (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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1043u ALA* 4.5 6.1 - - + +
1055u TRP* 4.8 24.8 - - + +
1059u CYS* 5.6 6.3 - - + -
1080u THR 2.9 17.9 + - - +
1081u PHE* 3.3 8.9 + - - +
1083u TYR* 1.3 76.2 - - - +
1085u ALA* 1.3 56.9 + - - +
1087u ALA* 3.1 7.6 + - - +
1088u ILE* 2.9 30.7 + - - +
1093u VAL* 5.7 6.1 - - + -
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Residues in contact with ALA1085 (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 3.0 16.5 + - - +
1082u GLY 3.9 4.0 - - - +
1084u ILE* 1.3 73.4 - - - +
1086u LYS* 1.3 59.5 + - - +
1089u GLY* 3.0 34.6 + - - +
1090u PRO* 3.7 24.8 - - + +
1093u VAL* 5.1 12.1 - - + +
1119u VAL* 4.4 17.5 - - + -
1123u CYS* 5.0 7.0 - - + +
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Residues in contact with LYS1086 (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 2.9 17.8 + - - +
1083u TYR* 3.6 10.5 - - + +
1084u ILE 3.3 0.2 - - - -
1085u ALA* 1.3 77.8 - - - +
1087u ALA* 1.3 61.3 + - - +
1089u GLY* 4.6 0.9 + - - -
1122u THR* 5.3 6.5 - - - -
1123u CYS* 4.9 15.8 - - + +
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Residues in contact with ALA1087 (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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1043u ALA* 5.0 1.3 - - - +
1047u ALA* 3.9 28.0 - - + +
1055u TRP* 5.7 5.2 - - + -
1083u TYR 2.9 13.7 + - - +
1084u ILE* 3.1 10.5 + - - +
1086u LYS* 1.3 79.7 - - - +
1088u ILE* 1.3 63.1 + - + +
1089u GLY 3.5 0.9 + - - -
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Residues in contact with ILE1088 (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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1052u ALA* 5.2 14.6 - - + +
1055u TRP* 5.1 12.3 - - + -
1056u MET* 6.2 0.9 - - + +
1084u ILE 2.9 14.8 + - - +
1087u ALA* 1.3 75.3 - - + +
1089u GLY* 1.3 63.1 + - - +
1092u ASP* 5.7 3.8 - - - +
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Residues in contact with GLY1089 (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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1085u ALA* 3.0 22.0 + - - +
1086u LYS 4.6 0.8 + - - -
1087u ALA 3.5 2.6 + - - -
1088u ILE* 1.3 83.3 - - - +
1090u PRO* 1.3 57.7 - - - +
1091u HIS* 3.1 12.1 + - - -
1092u ASP* 4.2 5.9 + - - +
1093u VAL* 4.8 5.0 + - - +
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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
------------------------------------------------------------
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