Contacts of the helix formed by residues 1014 - 1029 (chain B) in PDB entry 2BOA
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 SER1014 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B MET* 4.0 4.4 - - - +
97B GLU* 4.8 13.9 + - - -
1013B HIS* 1.3 77.5 - - - +
1015B LEU* 1.3 65.2 + - - +
1016B GLU* 3.7 11.0 + - - +
1017B ALA* 2.9 31.3 + - - +
1018B ILE* 3.1 9.9 + - - +
1120B GLN* 3.2 19.0 - - - +
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Residues in contact with LEU1015 (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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1014B SER* 1.3 73.1 - - - +
1016B GLU* 1.3 62.7 + - - +
1018B ILE* 3.8 7.4 - - + +
1019B TYR* 3.1 67.3 + - + +
1045B ARG* 3.8 28.5 - - - +
1110B VAL* 3.7 34.3 - - + -
1113B PRO* 4.1 5.4 - - + -
1116B TYR* 3.7 13.8 - - + -
1117B VAL* 3.7 26.8 - - + +
1120B GLN* 4.2 1.6 - - - +
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Residues in contact with GLU1016 (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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1019A TYR* 5.8 4.7 - - + -
1035A ARG* 3.6 20.8 + - - -
1046A PRO* 3.7 8.8 - - + +
1048A TYR* 2.4 37.7 + - - -
1014B SER* 3.1 11.3 + - - +
1015B LEU* 1.3 80.4 - - - +
1017B ALA* 1.3 58.7 + - - +
1019B TYR* 3.4 7.4 + - - +
1020B HIS* 3.1 27.0 + - + +
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Residues in contact with ALA1017 (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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1001B GLU* 5.2 3.6 - - - +
1007B PHE* 3.7 8.2 - - + -
1013B HIS* 3.8 24.2 - - + -
1014B SER* 2.9 19.0 + - - +
1016B GLU* 1.3 76.4 - - - +
1018B ILE* 1.3 61.5 + - - +
1020B HIS* 3.5 7.2 + - - +
1021B GLU* 2.8 30.0 + - - +
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Residues in contact with ILE1018 (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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1007B PHE* 4.8 3.8 - - - -
1013B HIS* 3.7 20.2 - - + +
1014B SER 3.1 7.6 + - - +
1015B LEU* 3.8 7.0 - - - +
1017B ALA* 1.3 76.3 - - - +
1019B TYR* 1.3 66.0 + - + +
1021B GLU* 2.9 8.3 + - - +
1022B MET* 2.8 38.7 + - + +
1076B GLN* 4.8 9.6 - - + +
1080B ILE* 4.5 21.3 - - + -
1109B PRO* 4.2 9.9 - - + -
1110B VAL* 4.0 28.9 - - + -
1116B TYR* 3.5 35.7 - - + +
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Residues in contact with TYR1019 (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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1016A GLU* 5.0 4.5 - - - +
1015B LEU* 3.1 50.3 + - + +
1016B GLU* 3.6 6.7 - - - +
1018B ILE* 1.3 78.1 - - + +
1020B HIS* 1.3 63.2 + - - +
1022B MET* 3.2 20.2 + - - +
1023B ASP 3.2 12.8 + - - -
1035B ARG* 3.2 23.8 + - - +
1045B ARG* 5.2 0.2 - - + -
1046B PRO* 2.6 39.2 + - + -
1047B MET* 4.2 0.3 - - - -
1048B TYR* 3.6 42.4 + + + -
1110B VAL* 4.8 10.0 + - + -
1113B PRO* 3.7 21.5 - - - +
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Residues in contact with HIS1020 (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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1020A HIS* 3.4 31.2 + + - -
1016B GLU* 3.1 11.5 + - + +
1017B ALA* 3.6 11.0 - - - +
1019B TYR* 1.3 76.4 - - - +
1021B GLU* 1.3 65.7 + - - +
1023B ASP* 3.1 4.9 + - - +
1024B ASN* 2.9 55.1 + - - +
1404B GOL 2.8 29.2 + - - +
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Residues in contact with GLU1021 (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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1007B PHE* 3.4 57.1 - - + +
1009B TYR* 2.5 33.1 + - + +
1017B ALA 2.8 12.7 + - - +
1018B ILE 2.9 4.6 + - - +
1020B HIS* 1.3 71.9 - - - +
1022B MET* 1.3 56.8 + - - +
1024B ASN* 3.1 21.6 + - - +
1025B ILE* 2.9 35.7 + - + +
1080B ILE* 4.2 5.8 - - + -
1084B ARG* 2.9 19.7 + - - -
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Residues in contact with MET1022 (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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1018B ILE* 2.8 18.1 + - - +
1019B TYR* 3.3 35.4 - - - +
1020B HIS 3.1 0.2 - - - -
1021B GLU* 1.3 78.3 - - - +
1023B ASP* 1.3 58.8 + - - +
1025B ILE* 3.8 2.2 + - - +
1026B ALA* 3.3 17.7 + - - +
1035B ARG* 3.9 9.1 - - + +
1048B TYR* 3.6 30.5 - - + +
1049B VAL 3.7 3.8 - - - -
1050B LEU* 3.4 53.8 - - + +
1080B ILE* 3.7 18.4 - - + -
1109B PRO* 3.7 23.6 - - + -
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Residues in contact with ASP1023 (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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1019B TYR 3.2 11.6 + - - +
1020B HIS* 3.1 11.5 + - + +
1022B MET* 1.3 74.5 - - - +
1024B ASN* 1.3 57.4 + - - +
1026B ALA* 3.6 6.5 - - - +
1027B ALA* 2.8 37.9 + - - +
1035B ARG* 4.2 19.5 + - - +
1404B GOL 3.0 41.1 + - - +
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Residues in contact with ASN1024 (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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1020B HIS* 2.9 43.2 + - - +
1021B GLU* 3.2 32.1 + - - +
1023B ASP* 1.3 75.2 - - - +
1025B ILE* 1.3 54.4 + - - +
1027B ALA* 3.1 7.2 + - - +
1028B ASP* 2.7 43.3 + - - +
1084B ARG* 4.7 3.1 - - - +
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Residues in contact with ILE1025 (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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1009B TYR* 4.0 5.6 - - - +
1021B GLU* 2.9 31.2 + - + +
1022B MET* 3.8 6.3 - - - +
1024B ASN* 1.3 74.0 - - - +
1026B ALA* 1.3 53.8 + - - +
1028B ASP* 2.9 9.7 + - - +
1029B PHE* 2.8 35.2 + - - +
1033B ALA* 4.3 8.5 - - + -
1050B LEU* 4.3 9.4 - - + -
1052B PHE* 4.4 0.9 - - + -
1080B ILE* 3.7 28.0 - - + +
1083B ALA* 3.9 17.5 - - + +
1084B ARG* 3.8 30.7 - - - +
1087B VAL* 3.8 30.7 - - + -
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Residues in contact with ALA1026 (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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1022B MET 3.3 12.2 + - - +
1023B ASP* 3.6 13.2 - - - +
1025B ILE* 1.3 77.7 - - - +
1027B ALA* 1.3 63.8 + - - +
1029B PHE 3.1 21.8 - - - -
1030B PRO* 3.2 9.0 - - - +
1033B ALA* 3.6 25.6 - - - +
1034B ARG* 4.1 2.0 - - - -
1035B ARG* 4.0 19.7 - - + +
1050B LEU* 4.1 2.0 - - + +
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Residues in contact with ALA1027 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023B ASP* 2.8 24.3 + - - +
1024B ASN* 3.6 7.6 - - - +
1026B ALA* 1.3 72.9 - - - +
1028B ASP* 1.3 61.2 + - - +
1030B PRO* 3.9 13.5 - - - +
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Residues in contact with ASP1028 (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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1024B ASN* 2.7 18.2 + - - +
1025B ILE* 3.4 9.4 - - - +
1027B ALA* 1.3 73.9 - - - +
1029B PHE* 1.3 82.5 + - + +
1030B PRO* 3.4 7.2 - - - +
1084B ARG* 3.4 27.2 + - - +
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Residues in contact with PHE1029 (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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1025B ILE 2.8 11.8 + - - +
1026B ALA 3.1 5.6 - - - +
1028B ASP* 1.3 99.8 - - + +
1030B PRO* 1.3 57.2 - - - +
1031B ASP* 3.0 5.2 - - - -
1032B LEU* 2.9 35.8 + - + -
1033B ALA* 3.0 12.2 + - - +
1084B ARG* 3.9 11.2 - - - -
1087B VAL* 3.4 59.9 - - + -
1088B SER* 4.7 6.3 - - - -
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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