Contacts of the helix formed by residues 1028 - 1045 (chain B) in PDB entry 5XA0
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 LEU1028 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026B GLY 3.5 0.8 + - - -
1027B ALA* 1.3 73.7 - - + +
1029B ASP* 1.3 66.2 + - - +
1030B PHE* 2.7 20.5 - - - +
1031B GLU* 5.6 1.8 - - + -
1032B HIS* 3.0 21.7 - - + +
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Residues in contact with ASP1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B GLY* 3.3 22.0 + - - +
1027B ALA 3.3 3.8 - - - -
1028B LEU* 1.3 72.7 - - - +
1030B PHE* 1.3 52.9 + - - +
1032B HIS* 5.0 0.7 - - - -
1033B ILE* 2.4 52.0 + - + +
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Residues in contact with PHE1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028B LEU* 2.7 21.0 - - - +
1029B ASP* 1.3 76.2 - - - +
1031B GLU* 1.3 62.8 + - + +
1032B HIS 2.6 19.5 + - - -
1033B ILE* 4.3 0.9 - - - +
1034B GLU* 4.6 5.4 - - + +
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Residues in contact with GLU1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028B LEU* 5.6 2.2 - - + -
1030B PHE* 1.3 76.8 - - + +
1032B HIS* 1.3 50.4 + - - +
1034B GLU* 4.0 13.3 - - - +
1035B GLU* 2.4 47.2 + - - +
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Residues in contact with HIS1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027B ALA 5.0 2.2 - - - +
1028B LEU* 3.0 25.4 - - + +
1029B ASP* 5.0 0.4 - - - -
1030B PHE 2.6 8.7 + - - -
1031B GLU* 1.3 73.2 - - - +
1033B ILE* 1.3 49.8 + - - +
1035B GLU* 3.2 5.5 - - - +
1036B GLN* 2.4 35.1 + - - +
1063B VAL* 5.3 14.1 - - + -
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Residues in contact with ILE1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B ASP* 2.4 51.5 + - + +
1030B PHE* 4.7 0.2 - - - -
1032B HIS* 1.3 70.4 - - - +
1034B GLU* 1.3 55.7 + - - +
1036B GLN* 3.1 10.3 - - + +
1037B ALA* 2.9 24.9 + - - +
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Residues in contact with GLU1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B ASP 3.9 1.4 + - - -
1030B PHE* 4.6 2.6 - - + +
1031B GLU* 3.8 17.1 + - - +
1033B ILE* 1.3 74.6 - - - +
1035B GLU* 1.3 60.5 + - - +
1036B GLN 3.0 1.3 - - - -
1037B ALA* 3.4 9.6 + - - +
1038B GLU* 3.0 24.1 + - - +
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Residues in contact with GLU1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031B GLU 2.4 37.0 + - - +
1032B HIS* 3.2 5.6 - - - +
1034B GLU* 1.3 69.2 - - - +
1036B GLN* 1.4 55.8 + - - +
1038B GLU* 3.2 13.4 - - + +
1039B GLY* 2.9 20.3 + - - -
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Residues in contact with GLN1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B HIS 2.4 29.5 + - - +
1033B ILE* 3.1 17.5 - - + +
1034B GLU 3.0 0.4 - - - -
1035B GLU* 1.4 67.5 - - - +
1037B ALA* 1.3 63.4 + - - +
1038B GLU 3.1 1.1 - - - -
1039B GLY* 2.9 13.1 + - - +
1040B ILE* 3.0 9.9 + - - +
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Residues in contact with ALA1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B ILE 2.9 15.3 + - - +
1034B GLU* 3.4 11.2 + - - +
1036B GLN* 1.3 71.4 - - - +
1038B GLU* 1.4 54.6 + - - +
1040B ILE* 2.8 29.2 + - + +
1041B PHE* 3.0 12.0 + - - +
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Residues in contact with GLU1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034B GLU 3.0 13.6 + - - +
1035B GLU* 3.2 19.5 - - + +
1036B GLN 3.1 0.2 - - - -
1037B ALA* 1.4 73.7 - - - +
1039B GLY* 1.3 56.2 + - - +
1041B PHE* 3.9 9.8 - - - +
1042B GLY* 2.9 23.2 + - - -
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Residues in contact with GLY1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B GLU 2.9 12.0 + - - -
1036B GLN* 2.9 7.8 + - - -
1038B GLU* 1.3 76.5 - - - +
1040B ILE* 1.3 59.7 - - - +
1041B PHE 3.3 0.2 - - - -
1042B GLY* 3.8 1.5 - - - -
1043B GLY* 2.8 26.4 + - - -
1082B LEU* 6.1 1.2 - - - +
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Residues in contact with ILE1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036B GLN 3.0 7.4 + - - +
1037B ALA* 2.8 24.1 + - - +
1039B GLY* 1.3 71.0 - - - +
1041B PHE* 1.3 58.7 + - - +
1043B GLY* 3.3 1.8 + - - -
1044B SER* 3.1 22.0 + - - -
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Residues in contact with PHE1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B ALA 3.0 10.6 + - - +
1038B GLU* 3.9 11.4 - - - +
1040B ILE* 1.3 73.7 - - - +
1042B GLY* 1.3 66.5 + - - +
1043B GLY 3.0 2.0 + - - -
1044B SER* 3.3 17.9 + - - -
1045B GLU* 4.2 3.5 + - - +
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Residues in contact with GLY1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B GLU 2.9 22.2 + - - -
1039B GLY* 4.1 2.0 - - - -
1041B PHE* 1.3 73.9 - - - +
1043B GLY* 1.3 58.7 + - - +
1044B SER 3.6 0.2 + - - -
1045B GLU* 3.6 16.7 + - - +
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Residues in contact with GLY1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039B GLY 2.8 19.6 + - - -
1040B ILE 3.7 2.0 - - - -
1041B PHE 3.0 0.4 - - - -
1042B GLY* 1.3 75.4 - - - +
1044B SER* 1.3 64.8 + - - +
1045B GLU 3.2 6.7 + - - +
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Residues in contact with SER1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B ILE 3.1 10.5 + - - -
1041B PHE* 3.3 12.2 + - - -
1043B GLY* 1.3 77.0 - - - +
1045B GLU* 1.3 64.0 + - - +
1046B GLU* 3.8 0.3 + - - -
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Residues in contact with GLU1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B PHE* 5.5 1.4 - - - +
741B ALA* 5.8 3.6 + - - +
1041B PHE 4.2 2.4 + - - +
1042B GLY* 3.6 15.3 + - - +
1043B GLY 3.2 7.1 - - - +
1044B SER* 1.3 82.7 - - - +
1046B GLU* 1.3 69.1 + - - +
1049B PRO* 6.5 1.1 - - + -
1052B LEU* 4.5 26.0 - - + +
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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