Contacts of the helix formed by residues 1066 - 1075 (chain A) in PDB entry 5JH5
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 HIS1066 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1065A MSE 1.3 82.5 + - - +
1067A ARG* 1.3 66.9 + - - +
1068A GLU 3.4 1.6 - - - -
1069A VAL* 3.1 25.8 + - + +
1070A TRP* 3.0 27.5 + - - -
101B PHE* 5.3 12.2 - + + +
105B LEU* 3.9 37.1 - - + +
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Residues in contact with ARG1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A MSE 3.8 3.4 + - - -
1066A HIS* 1.3 71.6 - - - +
1068A GLU* 1.3 82.2 + - + +
1070A TRP* 3.3 3.8 + - - +
1071A MSE 3.0 41.7 + - - +
1094A ARG 5.3 1.0 + - - -
1095A TRP* 3.1 64.0 - - + +
1098A ASP* 3.2 24.0 + - - +
1100A ARG* 2.8 24.3 - - - +
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Residues in contact with GLU1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A HIS* 3.4 0.4 - - - +
1067A ARG* 1.3 102.4 + - + +
1069A VAL* 1.3 66.2 + - + +
1071A MSE 3.3 8.6 + - - +
1072A ALA* 3.0 21.5 + - - +
1100A ARG* 4.2 14.1 + - - -
108B ASN* 5.4 4.9 + - - +
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Residues in contact with VAL1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A HIS* 3.1 27.0 + - + +
1068A GLU* 1.3 78.3 - - + +
1070A TRP* 1.3 67.4 + - + +
1072A ALA* 3.2 20.8 + - - +
1073A VAL* 3.2 10.8 + - + +
101B PHE* 5.2 10.5 - - + +
104B ILE* 3.6 31.9 - - + -
105B LEU* 3.5 32.1 - - + -
108B ASN* 4.2 18.4 - - - +
120B CYS* 4.8 0.2 - - - -
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Residues in contact with TRP1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A MSE 3.7 23.1 - - + +
1066A HIS* 3.0 30.3 + - - +
1067A ARG 3.7 6.5 - - - +
1069A VAL* 1.3 77.6 - - + +
1071A MSE 1.3 58.9 + - - +
1072A ALA 3.0 2.7 - - - -
1073A VAL* 3.0 20.5 + - + +
1074A PHE* 2.8 54.3 + + + -
1092A TRP* 3.7 37.9 - + - -
1095A TRP* 3.5 26.2 - + + -
101B PHE* 4.1 21.8 - + - -
123B VAL* 4.2 18.2 - - + -
127B ILE* 4.5 3.4 - - + -
139B PHE* 4.1 25.8 - + - -
141B ILE* 5.3 7.6 - - + -
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Residues in contact with MSE1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ARG* 3.0 45.2 + - + +
1068A GLU* 3.3 14.8 + - - +
1070A TRP* 1.3 77.1 - - + +
1072A ALA* 1.3 60.6 + - - +
1074A PHE* 4.0 9.9 - - - +
1075A SER* 3.2 23.6 + - - -
1095A TRP* 3.8 29.8 - - + +
1098A ASP* 3.8 16.2 - - + +
1100A ARG* 3.7 32.1 - - + +
1101A LEU* 4.1 22.5 - - + +
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Residues in contact with ALA1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A GLU 3.0 12.1 + - - +
1069A VAL* 3.2 13.9 - - - +
1070A TRP 3.0 0.4 - - - -
1071A MSE 1.3 76.0 - - - +
1073A VAL* 1.3 63.0 + - - +
1075A SER* 3.0 21.7 + - - -
1076A TYR* 3.3 14.7 - - + -
104B ILE* 5.4 0.4 - - + -
108B ASN* 5.5 2.7 - - - +
116B LEU* 5.2 11.9 - - + -
120B CYS* 3.7 20.2 - - - -
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Residues in contact with VAL1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A VAL* 3.2 11.4 + - + +
1070A TRP* 3.0 22.7 + - + +
1072A ALA* 1.3 77.1 - - - +
1074A PHE* 1.3 68.5 + - + +
1076A TYR* 3.1 20.1 + - - +
1077A LEU* 3.7 6.5 + - + +
101B PHE* 5.8 0.7 - - + -
104B ILE* 4.5 7.4 - - + -
120B CYS* 4.3 20.0 - - + -
123B VAL* 3.7 39.0 - - + -
124B ALA* 4.1 13.0 - - + +
127B ILE* 4.1 18.8 - - + -
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Residues in contact with PHE1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070A TRP* 2.8 53.5 + + + +
1071A MSE 4.0 17.3 - - - +
1072A ALA 3.3 0.2 - - - -
1073A VAL* 1.3 76.3 - - + +
1075A SER* 1.3 57.3 + - - +
1077A LEU* 2.9 49.0 + - + +
1082A LEU* 3.8 12.6 - - + +
1092A TRP* 3.6 38.6 - + - -
1095A TRP* 4.1 17.5 - + + -
1096A CYS* 3.6 29.4 - - - -
1101A LEU* 3.6 22.6 - - + +
127B ILE* 4.9 0.7 - - + -
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Residues in contact with SER1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071A MSE 3.2 15.1 + - - -
1072A ALA* 3.0 19.8 + - - -
1074A PHE* 1.3 75.6 - - - +
1076A TYR* 1.3 61.2 + - - +
1077A LEU 4.1 4.1 - - - +
1101A LEU* 3.6 17.9 - - - +
80B LYS* 3.4 43.5 + - - +
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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