Contacts of the helix formed by residues 1022 - 1029 (chain B) in PDB entry 2B7A
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 ALA1022 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020B TRP 3.9 0.2 + - - -
1021B TYR* 1.3 74.7 - - - +
1023B PRO* 1.3 76.8 - - + +
1024B GLU* 3.2 26.2 - - - +
1025B SER* 3.0 16.8 + - - +
1026B LEU* 3.1 11.0 + - - +
1035B SER* 3.9 13.6 + - - -
1038B TRP* 3.6 20.6 - - + +
1039B SER* 5.0 1.4 + - - -
1113B ARG* 3.6 11.9 - - - +
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Residues in contact with PRO1023 (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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1021B TYR 3.9 0.2 - - - -
1022B ALA* 1.3 85.0 - - + +
1024B GLU* 1.3 57.1 + - - +
1026B LEU* 3.2 15.6 + - + +
1027B THR* 2.9 35.3 + - + +
1038B TRP* 3.4 30.7 - - + -
1079B ILE* 6.0 4.3 - - + +
1082B LEU* 4.3 15.3 - - + -
1083B LYS* 6.1 0.9 - - - +
1108B ASN* 3.7 27.4 - - + +
1113B ARG* 3.7 8.3 - - - +
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Residues in contact with GLU1024 (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 ALA* 3.5 11.5 - - - +
1023B PRO* 1.3 71.6 - - - +
1025B SER* 1.3 59.5 + - - +
1027B THR* 3.4 10.1 - - - +
1028B GLU* 3.0 34.0 + - - +
1030B LYS* 3.2 38.1 + - + +
1032B SER* 4.5 3.6 + - - +
1035B SER* 3.8 9.9 + - - -
1108B ASN 4.9 1.2 - - - +
1110B VAL* 3.4 23.4 - - + +
1113B ARG* 2.8 44.2 + - - -
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Residues in contact with SER1025 (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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1012B GLU* 4.1 7.1 - - - +
1021B TYR* 3.9 14.6 - - - -
1022B ALA* 3.0 13.0 + - - +
1024B GLU* 1.3 75.3 - - - +
1026B LEU* 1.3 65.3 + - - +
1029B SER* 3.1 21.7 + - - +
1030B LYS 2.8 27.0 + - - +
1031B PHE* 3.5 31.2 - - - -
1035B SER* 3.7 14.0 - - - -
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Residues in contact with LEU1026 (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* 3.8 28.0 - - + +
1021B TYR* 3.5 39.3 - - + +
1022B ALA 3.1 6.8 + - - +
1023B PRO* 3.2 8.7 + - + +
1025B SER* 1.3 79.2 - - - +
1027B THR* 1.3 60.2 + - - +
1029B SER* 4.9 0.3 + - - -
1075B VAL* 4.1 15.5 - - + +
1078B LEU* 3.8 24.2 - - + -
1079B ILE* 3.8 28.6 - - + +
1082B LEU* 3.8 23.6 - - + -
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Residues in contact with THR1027 (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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1023B PRO* 2.9 20.9 + - + +
1024B GLU* 3.4 10.0 - - - -
1026B LEU* 1.3 79.4 - - - +
1028B GLU* 1.3 75.0 + - - +
1029B SER 3.7 0.2 - - - -
1079B ILE* 3.8 37.2 - - + -
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Residues in contact with GLU1028 (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 PTR 4.5 3.6 + - - -
1009B LYS* 4.0 25.3 + - - +
1024B GLU* 3.0 16.6 + - - +
1027B THR* 1.3 90.9 + - - +
1029B SER* 1.3 71.4 + - - +
1030B LYS* 3.3 35.5 + - + +
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Residues in contact with SER1029 (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 LYS* 3.3 18.4 - - - -
1010B VAL 3.4 21.3 + - - -
1012B GLU* 2.8 27.3 + - - +
1024B GLU 3.3 0.2 + - - -
1025B SER* 3.1 18.2 + - - +
1026B LEU 5.6 0.2 + - - -
1027B THR 3.7 1.0 - - - -
1028B GLU* 1.3 79.7 - - - +
1030B LYS* 1.3 59.5 + - - +
1031B PHE* 3.3 20.9 - - - -
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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