Contacts of the helix formed by residues 1065 - 1078 (chain E) in PDB entry 6BAA
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 ALA1065 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064E TYR* 1.3 81.8 - - - +
1066E MET* 1.3 55.2 + - - +
1068E PHE* 5.0 0.4 - - - -
1069E THR* 2.8 37.8 + - - +
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Residues in contact with MET1066 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064E TYR 3.3 4.1 - - - +
1065E ALA* 1.3 79.4 - - - +
1067E VAL* 1.3 61.8 + - + +
1069E THR* 3.7 3.1 - - - -
1070E LEU* 2.9 25.2 + - - +
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Residues in contact with VAL1067 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033E TRP* 5.1 12.2 - - + +
1036E LYS 5.9 1.1 - - - +
1037E TRP* 5.1 19.1 - - + +
1064E TYR* 4.5 1.8 + - - +
1066E MET* 1.3 80.2 - - + +
1068E PHE* 1.3 58.2 + - - +
1070E LEU* 3.3 11.3 + - + +
1071E LEU* 2.8 27.5 + - - +
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Residues in contact with PHE1068 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E VAL* 5.9 9.4 - - + -
563E VAL* 6.3 2.7 - - + -
1064E TYR 3.3 20.9 + - - +
1065E ALA* 3.9 1.5 + - - +
1066E MET 3.3 0.6 - - - -
1067E VAL* 1.3 76.0 - - - +
1069E THR* 1.3 59.6 + - - +
1071E LEU* 3.1 8.3 + - - +
1072E CYS* 2.9 28.1 + - - +
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Residues in contact with THR1069 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065E ALA* 2.8 24.0 + - - -
1066E MET* 3.7 3.4 - - - -
1068E PHE* 1.3 76.4 - - - +
1070E LEU* 1.3 59.0 + - - +
1072E CYS* 3.4 6.8 + - - +
1073E SER* 2.9 30.4 + - - -
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Residues in contact with LEU1070 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033E TRP* 5.8 6.5 - - + -
1066E MET 2.9 14.2 + - - +
1067E VAL* 3.3 14.6 - - + +
1068E PHE 3.2 0.2 - - - -
1069E THR* 1.3 76.9 - - - +
1071E LEU* 1.3 56.9 + - - +
1073E SER* 3.4 6.9 + - - -
1074E LEU* 2.8 29.2 + - - +
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Residues in contact with LEU1071 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556E LEU* 5.4 4.9 - - + +
1030E ILE* 5.7 9.4 - - + +
1033E TRP* 5.9 8.5 - - + +
1034E LEU* 6.1 2.9 - - + +
1067E VAL 2.8 15.7 + - - +
1068E PHE* 3.1 11.8 + - - +
1070E LEU* 1.3 70.8 - - - +
1072E CYS* 1.3 60.7 + - - +
1074E LEU* 3.2 7.5 + - - +
1075E GLY* 2.9 25.1 + - - -
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Residues in contact with CYS1072 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556E LEU* 5.3 10.1 - - + -
1068E PHE 2.9 15.1 + - - +
1069E THR* 3.8 7.2 - - - +
1071E LEU* 1.3 75.2 - - - +
1073E SER* 1.3 62.6 + - - +
1075E GLY* 3.1 2.3 + - - +
1076E ILE* 3.1 24.1 + - - +
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Residues in contact with SER1073 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069E THR 2.9 18.0 + - - -
1070E LEU* 3.6 7.6 - - - -
1072E CYS* 1.3 77.2 - - - +
1074E LEU* 1.3 60.9 + - - +
1076E ILE* 3.8 11.7 + - - +
1077E VAL* 4.0 8.8 + - - +
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Residues in contact with LEU1074 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026E VAL* 4.8 13.2 - - + +
1029E ALA* 5.6 3.4 - - + -
1030E ILE* 4.9 20.9 - - + +
1070E LEU 2.8 18.2 + - - +
1071E LEU* 3.5 8.5 - - - +
1072E CYS 3.2 0.2 - - - -
1073E SER* 1.3 78.0 - - - +
1075E GLY* 1.3 57.9 + - - +
1077E VAL* 3.1 26.1 + - - +
1078E LEU* 4.1 2.9 + - - +
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Residues in contact with GLY1075 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E ILE* 3.3 33.7 - - - +
556E LEU* 5.5 5.8 - - - -
1030E ILE* 5.9 4.5 - - - -
1071E LEU 2.9 15.0 + - - -
1072E CYS* 3.1 3.3 + - - -
1074E LEU* 1.3 74.8 - - - +
1076E ILE* 1.3 65.6 + - - +
1077E VAL 3.2 0.2 - - - -
1078E LEU* 4.0 7.8 + - - +
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Residues in contact with ILE1076 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072E CYS 3.1 15.0 + - - +
1073E SER* 4.0 8.5 - - - +
1074E LEU 3.2 0.6 - - - -
1075E GLY* 1.3 78.5 - - - +
1077E VAL* 1.3 61.7 + - - +
1078E LEU 3.2 10.7 + - - +
1079E CYS* 5.0 1.4 - - - +
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Residues in contact with VAL1077 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023E LYS* 5.6 1.0 - - - +
1026E VAL* 4.7 12.6 - - + -
1073E SER 4.0 5.5 + - - +
1074E LEU* 3.1 18.1 + - - +
1076E ILE* 1.3 78.9 - - - +
1078E LEU* 1.3 61.1 + - - +
1079E CYS* 3.3 12.0 + - - +
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Residues in contact with LEU1078 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545E PHE* 4.5 7.1 - - - -
548E THR 6.1 0.2 - - - +
549E ALA* 4.9 9.4 - - + +
552E ILE* 4.3 27.4 - - + -
1023E LYS* 4.6 23.3 - - + +
1026E VAL* 5.2 5.2 - - + +
1027E LEU* 6.2 0.4 - - + +
1074E LEU 4.1 3.3 + - - +
1075E GLY* 4.0 8.5 + - - +
1076E ILE 3.2 13.1 + - - +
1077E VAL* 1.3 75.9 - - - +
1079E CYS* 1.3 60.1 + - - +
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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