Contacts of the helix formed by residues 1028 - 1046 (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 HIS1028 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987u PRO* 3.7 30.1 - - + -
1026u ASN* 3.2 5.7 - - + +
1027u ARG* 1.3 78.7 - - - +
1029u GLU* 1.3 60.2 + - - +
1030u LYS* 3.4 2.2 - - + +
1031u VAL* 3.4 12.2 + - + +
1032u GLN* 2.9 29.2 + - - +
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Residues in contact with GLU1029 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027u ARG 3.9 2.2 + - - +
1028u HIS* 1.3 71.3 - - - +
1030u LYS* 1.3 60.5 + - - +
1032u GLN* 3.7 6.0 - - - +
1033u GLU* 2.9 29.3 + - - +
1068u ALA* 5.6 10.1 - - + -
1069u HIS 6.0 2.9 - - - +
1070u LYS* 5.2 14.6 - - + -
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Residues in contact with LYS1030 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987u PRO 5.4 3.8 - - - +
988u GLU* 6.2 1.8 - - - -
991u GLY* 4.6 12.6 - - - -
1028u HIS* 3.4 2.1 - - + +
1029u GLU* 1.3 75.4 - - - +
1031u VAL* 1.3 61.1 + - - +
1033u GLU* 3.3 5.7 + - - +
1034u ASN* 3.0 32.4 + - - +
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Residues in contact with VAL1031 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987u PRO* 4.8 13.4 + - + +
990u LEU* 5.3 6.7 - - + -
991u GLY* 4.5 13.3 - - - +
1023u ILE 5.2 4.9 - - - +
1026u ASN* 4.7 16.4 - - + -
1028u HIS* 3.4 20.6 + - + +
1029u GLU 3.4 0.2 - - - -
1030u LYS* 1.3 78.1 - - - +
1032u GLN* 1.3 56.4 + - - +
1034u ASN* 4.1 1.2 - - - +
1035u CYS* 2.9 33.9 + - - +
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Residues in contact with GLN1032 (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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1024u LEU* 5.9 4.5 - - - +
1026u ASN 4.6 10.7 + - - +
1027u ARG* 5.7 0.9 - - - -
1028u HIS 2.9 17.8 + - - +
1029u GLU* 3.7 8.1 - - - +
1031u VAL* 1.3 76.0 - - - +
1033u GLU* 1.3 56.9 + - - +
1035u CYS* 3.8 4.2 - - - +
1036u ILE* 2.9 34.0 + - - +
1065u LEU* 5.7 7.4 - - + +
1073u ILE* 5.2 12.0 - - + +
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Residues in contact with GLU1033 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029u GLU 2.9 18.5 + - - +
1030u LYS* 3.7 7.2 - - - +
1031u VAL 3.3 0.2 - - - -
1032u GLN* 1.3 77.0 - - - +
1034u ASN* 1.3 58.0 + - - +
1036u ILE* 3.9 1.3 - - - +
1037u ASP* 3.0 31.1 + - - +
1072u ALA* 5.8 5.8 - - + -
1073u ILE* 5.0 18.8 - - + +
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Residues in contact with ASN1034 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991u GLY* 4.1 10.8 - - - +
994u LEU* 3.7 28.5 - - + +
995u GLY* 4.2 9.0 - - - +
998u LYS* 5.3 4.5 - - + +
1030u LYS 3.0 16.3 + - - +
1031u VAL 4.3 1.1 - - - +
1033u GLU* 1.3 75.9 - - - +
1035u CYS* 1.3 57.9 + - - +
1037u ASP* 3.5 5.2 + - - +
1038u LEU* 3.0 29.6 + - - +
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Residues in contact with CYS1035 (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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994u LEU* 4.7 5.7 - - + +
1020u LEU* 5.4 9.7 - - + +
1023u ILE* 5.0 16.2 - - + +
1024u LEU* 5.0 13.2 - - + +
1031u VAL 2.9 21.8 + - - +
1032u GLN* 3.8 5.2 - - - +
1034u ASN* 1.3 77.8 - - - +
1036u ILE* 1.3 57.1 + - - +
1038u LEU* 3.3 6.3 + - - +
1039u VAL* 2.9 27.5 + - - +
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Residues in contact with ILE1036 (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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1032u GLN 2.9 18.1 + - - +
1033u GLU* 4.5 1.3 - - - +
1035u CYS* 1.3 73.2 - - - +
1037u ASP* 1.3 59.9 + - - +
1039u VAL* 3.7 9.2 - - + +
1040u GLY* 2.9 24.6 + - - -
1065u LEU* 6.5 0.9 - - + -
1073u ILE* 5.7 4.3 - - + +
1076u ALA* 5.2 12.2 - - + +
1077u THR* 5.3 17.5 - - - -
1080u THR* 4.9 7.5 - - - -
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Residues in contact with ASP1037 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998u LYS* 6.1 3.6 - - + -
1033u GLU 3.0 19.4 + - - +
1034u ASN* 3.8 6.3 - - - +
1035u CYS 3.2 0.2 - - - -
1036u ILE* 1.3 76.3 - - - +
1038u LEU* 1.3 59.7 + - - +
1040u GLY* 3.3 2.0 + - - -
1041u ARG* 3.0 26.7 + - - +
1076u ALA* 5.4 9.8 - - + +
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Residues in contact with LEU1038 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994u LEU* 5.4 3.8 - - + +
997u LEU* 6.1 0.7 - - + -
998u LYS* 5.0 18.1 - - + +
1034u ASN 3.0 17.0 + - - +
1035u CYS* 3.7 5.4 - - - +
1037u ASP* 1.3 76.1 - - - +
1039u VAL* 1.3 57.0 + - - +
1041u ARG* 3.3 8.0 + - - +
1042u ILE* 2.9 28.9 + - - +
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Residues in contact with VAL1039 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020u LEU* 6.2 3.6 - - + -
1035u CYS 2.9 16.8 + - - +
1036u ILE* 3.7 10.5 - - + +
1037u ASP 3.3 0.2 - - - -
1038u LEU* 1.3 77.2 - - - +
1040u GLY* 1.3 56.5 + - - +
1042u ILE* 3.4 7.4 + - - +
1043u ALA* 2.8 30.7 + - - +
1080u THR* 5.2 6.3 - - - -
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Residues in contact with GLY1040 (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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1036u ILE 2.9 17.7 + - - -
1037u ASP* 3.8 2.5 - - - -
1038u LEU 3.3 0.2 - - - -
1039u VAL* 1.3 72.4 - - - +
1041u ARG* 1.3 61.1 + - - +
1043u ALA* 3.7 7.4 - - - +
1044u ASP* 3.0 30.7 + - - +
1076u ALA 6.0 0.4 - - - -
1079u ASN 5.9 0.2 - - - -
1080u THR* 4.6 15.0 - - - -
1083u TYR* 5.1 1.3 - - - +
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Residues in contact with ARG1041 (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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1001u VAL* 5.7 9.0 - - + -
1037u ASP 3.0 14.1 + - - +
1038u LEU* 3.3 11.6 + - - +
1040u GLY* 1.3 76.0 - - - +
1042u ILE* 1.3 57.0 + - - +
1044u ASP* 3.9 1.6 - - - +
1045u ARG* 3.0 33.6 + - - +
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Residues in contact with ILE1042 (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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1013u ILE* 5.9 6.1 - - + -
1017u LEU* 5.5 12.3 - - + -
1038u LEU 2.9 16.5 + - - +
1039u VAL* 3.7 7.6 - - - +
1041u ARG* 1.3 77.1 - - - +
1043u ALA* 1.3 57.8 + - - +
1046u GLY* 2.6 45.2 + - - +
1047u ALA* 3.4 0.5 + - - -
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Residues in contact with ALA1043 (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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1039u VAL 2.8 20.3 + - - +
1040u GLY* 3.2 8.9 + - - +
1042u ILE* 1.3 73.5 - - - +
1044u ASP* 1.3 59.0 + - - +
1047u ALA* 4.2 16.3 - - - +
1080u THR* 4.5 7.6 - - - +
1083u TYR* 3.4 38.4 - - + +
1084u ILE* 4.5 5.2 - - + +
1087u ALA* 5.0 0.3 - - - +
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Residues in contact with ASP1044 (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 3.0 15.1 + - - +
1041u ARG* 4.7 1.8 - - - +
1043u ALA* 1.3 78.6 - - - +
1045u ARG* 1.3 60.5 + - - +
1046u GLY 4.0 0.2 - - - -
1047u ALA* 5.5 1.1 - - - -
1083u TYR* 4.3 11.4 - - + -
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Residues in contact with ARG1045 (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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1006u MET* 4.7 18.6 - - + +
1041u ARG 3.0 15.7 + - - +
1042u ILE* 4.9 0.2 - - - -
1044u ASP* 1.3 80.2 - - - +
1046u GLY* 1.3 56.8 + - - +
1047u ALA 3.9 1.8 - - - -
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Residues in contact with GLY1046 (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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1006u MET* 5.9 3.1 - - - -
1013u ILE* 4.8 10.4 - - - +
1042u ILE* 2.6 28.0 + - - +
1045u ARG* 1.3 74.5 - - - +
1047u ALA* 1.3 56.3 + - - +
1048u GLU* 3.1 11.2 + - - -
1049u TYR* 3.5 17.7 + - - +
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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
------------------------------------------------------------
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