Contacts of the helix formed by residues 1033 - 1043 (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 GLU1033 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1030r ARG* 3.2 18.3 + - + +
1031r GLU 3.2 0.6 - - - -
1032r GLU* 1.3 76.5 - - + +
1034r LYS* 1.3 56.4 + - - +
1035r LEU 3.0 5.6 - - - -
1036r GLU* 3.0 24.0 + - + +
1037r LEU* 3.0 15.4 + - + +
1074r GLY* 6.2 3.8 - - - -
1076r ALA* 6.0 4.9 - - + -
1077r LEU* 5.3 14.6 - - + +
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Residues in contact with LYS1034 (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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1029r VAL* 6.0 4.7 - - + -
1030r ARG 3.3 10.2 + - - +
1031r GLU* 3.1 16.1 + - - +
1033r GLU* 1.3 77.1 - - - +
1035r LEU* 1.3 60.4 + - - +
1036r GLU 3.5 0.2 - - - -
1037r LEU* 4.1 9.8 - - - +
1038r GLN* 3.6 19.8 + - - +
1053r GLU* 5.6 11.2 - - + -
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Residues in contact with LEU1035 (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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1031r GLU 4.2 2.0 + - - +
1032r GLU 3.9 13.6 + - - +
1033r GLU 3.0 0.2 - - - -
1034r LYS* 1.3 80.6 - - - +
1036r GLU* 1.3 61.8 + - - +
1038r GLN* 3.8 8.2 + - - +
1039r LYS* 3.9 9.2 + - - +
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Residues in contact with GLU1036 (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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1032r GLU 4.8 0.2 + - - -
1033r GLU* 3.0 12.2 + - + +
1035r LEU* 1.3 75.6 - - - +
1037r LEU* 1.3 66.7 + - - +
1038r GLN 3.1 2.0 - - - -
1039r LYS* 2.9 19.7 + - - +
1040r LEU* 2.9 13.5 + - - +
1073r GLU* 5.7 11.4 - - + +
1074r GLY 5.9 2.5 - - - +
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Residues in contact with LEU1037 (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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1033r GLU* 3.0 17.0 + - + +
1034r LYS* 4.3 9.2 - - - +
1036r GLU* 1.3 75.7 - - - +
1038r GLN* 1.3 57.5 + - - +
1040r LEU* 3.4 8.5 + - - +
1041r LEU* 2.8 29.7 + - - +
1053r GLU* 6.5 1.6 - - + -
1058r LYS* 5.9 7.6 - - + -
1061r VAL* 5.0 7.7 - - + +
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Residues in contact with GLN1038 (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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1034r LYS 3.6 16.5 + - - +
1035r LEU* 3.9 6.3 - - - +
1036r GLU 3.1 0.8 - - - -
1037r LEU* 1.3 75.6 - - - +
1039r LYS* 1.3 65.5 + - - +
1041r LEU* 3.0 18.0 + - - +
1042r GLU* 3.1 13.7 + - - +
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Residues in contact with LYS1039 (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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1035r LEU 3.9 6.3 + - - +
1036r GLU* 2.9 13.4 + - - +
1038r GLN* 1.3 75.4 - - - +
1040r LEU* 1.3 63.8 + - - +
1042r GLU* 3.0 16.9 + - - +
1043r ARG* 3.2 14.1 + - - +
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Residues in contact with LEU1040 (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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1036r GLU 2.9 11.5 + - - +
1037r LEU* 3.6 13.0 - - - +
1039r LYS* 1.3 76.4 - - - +
1041r LEU* 1.3 61.2 + - - +
1043r ARG* 3.3 15.3 + - - +
1044r VAL* 3.4 15.1 + - - +
1061r VAL* 4.9 15.9 - - + +
1065r ALA* 5.6 8.1 - - + -
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Residues in contact with LEU1041 (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 2.8 18.8 + - - +
1038r GLN* 3.0 11.4 + - - +
1040r LEU* 1.3 78.7 - - - +
1042r GLU* 1.3 59.8 + - - +
1043r ARG 3.6 0.2 + - - -
1044r VAL* 3.8 13.8 + - - +
1048r VAL* 6.0 7.2 - - + +
1061r VAL* 4.9 11.9 - - + -
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Residues in contact with GLU1042 (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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1038r GLN 3.1 8.7 + - - +
1039r LYS* 3.0 9.9 + - - +
1041r LEU* 1.3 77.7 - - - +
1043r ARG* 1.3 58.3 + - - +
1044r VAL 3.4 6.2 + - - +
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Residues in contact with ARG1043 (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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1039r LYS 3.2 13.1 + - - +
1040r LEU* 3.3 9.8 + - - +
1042r GLU* 1.3 78.8 - - - +
1044r VAL* 1.3 58.6 + - - +
1045r PRO 4.1 0.9 - - - -
1068r SER* 5.5 5.7 - - - -
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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
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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