Contacts of the helix formed by residues 1054 - 1068 (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 GLU1054 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029r VAL* 4.5 10.9 - - - +
1051r SER* 5.8 1.6 - - - -
1052r ILE 3.3 10.0 + - - +
1053r GLU* 1.3 74.3 - - - +
1055r PRO* 1.3 67.5 - - - +
1056r SER* 3.3 9.7 + - - +
1057r ALA* 3.3 8.8 + - - +
1058r LYS* 3.4 11.8 + - - +
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Residues in contact with PRO1055 (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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1019r SER 5.7 0.4 - - - -
1024r PHE 5.7 1.6 - - - +
1025r LYS 6.1 0.2 - - - +
1027r ILE* 3.3 29.4 - - + +
1028r THR* 4.8 7.6 - - - -
1029r VAL* 5.2 1.4 - - - +
1054r GLU* 1.3 74.7 - - - +
1056r SER* 1.3 64.8 + - - +
1058r LYS* 3.1 8.2 + - + +
1059r ILE* 2.9 25.4 + - - +
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Residues in contact with SER1056 (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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1016r ARG* 5.5 5.2 - - - -
1019r SER* 3.6 29.3 - - - -
1020r LEU* 6.3 0.7 - - - -
1051r SER* 4.6 16.2 - - - -
1054r GLU* 3.2 6.5 - - - +
1055r PRO* 1.3 79.1 - - - +
1057r ALA* 1.3 57.6 + - - +
1059r ILE* 3.4 0.6 + - - -
1060r ASN* 2.9 31.4 + - - +
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Residues in contact with ALA1057 (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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1048r VAL* 5.5 8.5 - - + +
1051r SER* 4.6 12.0 - - - +
1052r ILE 3.0 32.1 + - - +
1053r GLU* 4.3 4.7 - - - -
1054r GLU 3.3 5.5 + - - +
1055r PRO 3.2 0.4 - - - -
1056r SER* 1.3 77.7 - - - +
1058r LYS* 1.3 59.4 + - - +
1060r ASN* 3.2 5.2 + - - +
1061r VAL* 2.8 35.0 + - + +
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Residues in contact with LYS1058 (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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1027r ILE* 6.5 1.3 - - + -
1028r THR 5.2 3.8 - - - +
1029r VAL* 4.5 17.5 - - + -
1037r LEU* 5.9 7.9 - - + -
1054r GLU 3.4 8.5 + - - +
1055r PRO* 3.1 11.3 + - + +
1057r ALA* 1.3 78.1 - - - +
1059r ILE* 1.3 58.8 + - - +
1061r VAL* 4.1 2.9 - - - +
1062r LEU* 2.9 31.4 + - - +
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Residues in contact with ILE1059 (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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1019r SER* 4.3 20.4 - - - +
1024r PHE* 5.5 9.9 - - + -
1055r PRO 2.9 15.3 + - - +
1056r SER 3.8 2.9 - - - +
1058r LYS* 1.3 78.6 - - - +
1060r ASN* 1.3 61.8 + - - +
1062r LEU* 3.3 6.5 + - - +
1063r LEU* 2.9 23.4 + - - +
1084r VAL* 5.0 13.2 - - + +
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Residues in contact with ASN1060 (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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1015r PHE* 4.9 19.7 - - + +
1016r ARG* 5.6 2.0 - - - +
1019r SER* 4.5 9.1 - - - -
1048r VAL* 4.9 13.2 - - + -
1056r SER 2.9 17.8 + - - +
1057r ALA* 3.6 6.7 - - - +
1059r ILE* 1.3 76.3 - - - +
1061r VAL* 1.3 64.0 + - - +
1063r LEU* 3.0 18.3 + - - +
1064r GLN* 3.0 13.8 + - - +
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Residues in contact with VAL1061 (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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1037r LEU* 5.0 7.0 - - + +
1040r LEU* 4.9 15.2 - - + +
1041r LEU* 4.9 20.0 - - + -
1044r VAL* 5.6 3.1 - - - -
1048r VAL* 5.6 6.4 - - + +
1057r ALA 2.8 19.1 + - - +
1058r LYS* 4.2 3.1 - - - +
1060r ASN* 1.3 73.8 - - - +
1062r LEU* 1.3 55.8 + - - +
1064r GLN* 3.8 8.2 - - - +
1065r ALA* 2.9 30.0 + - - +
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Residues in contact with LEU1062 (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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1058r LYS 2.9 20.2 + - - +
1059r ILE* 3.4 8.3 - - - +
1060r ASN 3.0 0.2 - - - -
1061r VAL* 1.3 75.3 - - - +
1063r LEU* 1.3 65.7 + - - +
1065r ALA* 3.0 8.6 + - - +
1066r PHE* 2.9 23.4 + - - +
1077r LEU 5.9 0.2 - - - +
1080r ASP* 5.8 1.1 - - + -
1081r MET* 4.4 29.0 - - + +
1084r VAL* 5.0 6.3 - - + -
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Residues in contact with LEU1063 (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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1015r PHE* 6.5 0.7 - - + -
1059r ILE 2.9 12.8 + - - +
1060r ASN* 3.0 10.3 + - - +
1062r LEU* 1.3 74.5 - - - +
1064r GLN* 1.3 63.6 + - - +
1066r PHE* 3.2 9.2 + - - +
1067r ILE* 2.9 23.0 + - - +
1084r VAL* 5.4 7.7 - - + +
1085r THR* 5.9 5.4 - - - +
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Residues in contact with GLN1064 (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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1044r VAL* 4.2 25.4 - - + -
1045r PRO 5.7 0.9 - - - -
1046r ILE* 5.8 7.2 - - + +
1060r ASN 3.0 11.7 + - - +
1061r VAL* 3.8 8.5 - - - +
1063r LEU* 1.3 78.4 - - - +
1065r ALA* 1.3 52.2 + - - +
1067r ILE* 3.6 5.4 - - - +
1068r SER* 2.6 41.4 + - - -
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Residues in contact with ALA1065 (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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1040r LEU* 5.6 9.0 - - + -
1061r VAL 2.9 19.7 + - - +
1062r LEU* 3.3 8.1 - - - +
1064r GLN* 1.3 76.6 - - - +
1066r PHE* 1.3 57.2 + - - +
1068r SER* 3.5 3.4 - - - -
1069r GLN 2.8 23.0 + - - -
1070r LEU* 2.8 35.9 + - + +
1081r MET* 6.3 1.1 - - + -
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Residues in contact with PHE1066 (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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1062r LEU 2.9 11.9 + - - +
1063r LEU* 3.4 9.9 - - - +
1065r ALA* 1.3 79.1 - - - +
1067r ILE* 1.3 62.6 + - - +
1069r GLN* 3.1 13.7 + - - +
1070r LEU 5.0 1.8 - - - +
1081r MET* 5.6 7.0 - - + +
1085r THR* 4.4 22.2 - - - -
1121r ARG* 4.5 10.2 - - - +
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Residues in contact with ILE1067 (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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1063r LEU 2.9 15.8 + - - +
1064r GLN* 3.8 6.3 - - - +
1066r PHE* 1.3 72.9 - - - +
1068r SER* 1.3 59.4 + - - +
1069r GLN* 2.9 9.3 + - - +
1117r MET* 4.4 20.0 - - + +
1118r ILE* 5.5 3.6 - - - +
1121r ARG* 3.4 28.3 - - - +
1122r MET* 3.8 12.9 - - - +
1123r TRP* 4.6 2.6 + - + +
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Residues in contact with SER1068 (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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2316A ASN 4.8 11.2 - - - +
1043r ARG 5.5 6.5 - - - -
1044r VAL* 6.2 2.5 - - - -
1064r GLN* 2.6 23.5 + - - -
1065r ALA* 4.0 5.2 - - - -
1067r ILE* 1.3 70.8 - - - +
1069r GLN* 1.3 71.8 + - - +
1070r LEU* 4.9 3.5 - - - +
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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