Contacts of the helix formed by residues 1142 - 1146 (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 ASP1142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069B HIS* 2.9 22.6 + - - -
1127B ARG* 2.9 28.9 + - - -
1128B LYS* 3.7 7.7 - - - +
1141B ALA* 1.3 70.4 - - - +
1143B PRO* 1.3 66.1 - - - +
1144B ASN* 2.9 9.9 + - - +
1145B ARG* 3.0 41.4 + - + +
1146B ASN* 3.4 10.9 + - - +
1163B GLU 3.6 13.6 - - - +
1164B VAL* 3.6 10.1 - - - +
1165B TYR 2.8 18.9 + - - +
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Residues in contact with PRO1143 (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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1068B ILE* 3.4 42.2 - - + +
1069B HIS* 4.0 10.3 - - + -
1112B ASN* 4.0 7.0 - - + +
1128B LYS* 4.0 8.5 - - - -
1129B THR* 4.0 21.5 - - + -
1141B ALA 3.2 8.9 - - - +
1142B ASP* 1.3 89.4 - - - +
1144B ASN* 1.3 55.0 + - - +
1145B ARG 3.2 0.2 - - - -
1146B ASN* 3.2 18.3 + - + +
1147B TRP* 3.1 24.1 + - - -
1173B GLU* 5.1 1.3 - - + -
1175B GLU* 6.1 2.2 - - + -
1176B VAL* 3.6 12.6 - - + +
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Residues in contact with ASN1144 (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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1068B ILE* 4.3 6.1 - - + +
1069B HIS* 3.5 24.1 - - + +
1142B ASP* 2.9 3.0 + - - +
1143B PRO* 1.3 75.4 - - - +
1145B ARG* 1.3 78.1 + - - +
1147B TRP* 4.0 4.5 + - - -
1194B ASP* 3.6 6.4 - - - +
1196B HIS* 4.1 17.8 + - - -
1251B SER 4.0 0.3 - - - +
1252B GLY 3.2 13.0 - - - +
1253B SER* 3.3 22.5 - - - -
1254B SER* 3.2 33.0 + - - +
1268B THR* 5.9 0.8 + - - -
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Residues in contact with ARG1145 (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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1069B HIS* 5.4 3.2 - - - -
1127B ARG* 5.5 2.8 - - - +
1142B ASP* 3.0 43.1 + - + +
1144B ASN* 1.3 99.4 + - - +
1146B ASN* 1.3 58.7 + - - +
1151B PHE* 3.7 7.8 - - - -
1152B ALA 5.1 1.0 + - - -
1155B GLY 3.4 8.1 + - - +
1156B ALA* 3.6 24.6 - - + +
1164B VAL* 3.6 17.3 - - - +
1166B HIS* 3.6 23.7 - - - +
1248B TYR* 2.6 42.4 + - - -
1250B ALA* 3.2 27.7 - - - +
1251B SER 3.6 9.9 - - - +
1252B GLY* 3.2 16.0 - - - -
1253B SER* 5.1 0.8 - - - -
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Residues in contact with ASN1146 (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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1142B ASP 3.4 9.2 + - - +
1143B PRO* 3.2 15.8 + - + +
1145B ARG* 1.3 77.3 - - - +
1147B TRP* 1.3 61.8 + - - +
1151B PHE* 4.4 2.0 - - - -
1166B HIS 2.7 25.3 + - - +
1169B HIS 3.2 11.3 + - - -
1170B ALA* 3.4 3.1 - - - -
1171B ASN* 2.7 36.7 + - - -
1172B SER* 3.0 27.1 + - - -
1173B GLU* 3.0 40.3 + - + +
1176B VAL* 3.8 7.2 - - + +
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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