Contacts of the helix formed by residues 1173 - 1187 (chain A) 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 GLU1173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1042A PHE* 6.0 0.2 - - - +
1129A THR* 2.5 36.8 + - + -
1131A SER* 2.9 23.6 + - - -
1141A ALA* 3.5 23.9 - - + +
1143A PRO* 4.8 2.5 - - + -
1146A ASN* 3.0 27.4 + - + +
1168A PRO* 4.5 5.4 - - - +
1171A ASN 3.7 0.9 - - - +
1172A SER* 1.3 98.0 + - - +
1174A VAL* 1.3 57.4 + - - +
1175A GLU* 3.1 10.3 - - - +
1176A VAL* 2.8 35.0 + - + +
1177A LYS 3.0 10.6 + - - -
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Residues in contact with VAL1174 (chain A).
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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1040A HIS 3.2 21.5 - - - +
1041A SER 3.7 3.4 - - - +
1042A PHE* 3.7 34.5 - - + +
1172A SER 3.3 10.7 + - - +
1173A GLU* 1.3 70.6 - - - +
1175A GLU* 1.3 61.3 + - - +
1177A LYS* 3.9 9.5 - - + +
1178A SER* 2.8 35.0 + - - +
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Residues in contact with GLU1175 (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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1040A HIS 4.8 0.2 - - - -
1041A SER* 3.8 6.3 - - - -
1042A PHE* 3.0 35.7 + - - +
1047A MET* 3.7 30.7 - - + +
1111A ALA 3.7 19.1 - - - +
1112A ASN* 4.8 6.1 - - + +
1113A PRO* 4.1 7.1 - - + +
1114A ASP* 4.0 6.6 - - - +
1129A THR* 3.9 22.8 - - + +
1130A ARG 5.1 0.2 + - - -
1143A PRO* 6.2 1.8 - - + -
1173A GLU* 3.8 11.8 - - + +
1174A VAL* 1.3 87.9 + - - +
1176A VAL* 1.3 62.4 + - + +
1178A SER* 3.6 3.6 - - - -
1179A VAL* 3.5 25.3 + - - +
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Residues in contact with VAL1176 (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 ILE* 5.1 2.5 - - + -
1143A PRO* 3.5 33.4 - - + +
1146A ASN* 3.6 17.7 - - - +
1147A TRP* 3.5 46.7 - - + +
1171A ASN* 3.9 17.7 - - - +
1173A GLU* 2.8 22.3 + - + +
1175A GLU* 1.3 71.6 - - + +
1177A LYS* 1.3 53.9 + - - +
1179A VAL* 3.0 5.2 + - - +
1180A VAL* 2.8 33.2 + - + +
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Residues in contact with LYS1177 (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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1171A ASN* 3.4 40.3 + - + +
1173A GLU 3.0 8.6 + - - +
1174A VAL* 3.9 10.8 - - + +
1176A VAL* 1.3 76.4 - - - +
1178A SER* 1.3 52.8 + - - +
1180A VAL* 3.6 10.7 - - + -
1181A ASP* 2.7 72.4 + - - +
1401A NAG 6.0 0.2 + - - -
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Residues in contact with SER1178 (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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1038A ILE* 4.0 27.2 + - - +
1039A GLY* 3.4 22.8 - - - -
1040A HIS 3.8 6.9 + - - -
1047A MET* 4.7 4.5 - - - -
1174A VAL* 2.8 23.9 + - - +
1175A GLU* 3.6 10.1 - - - -
1176A VAL 3.2 0.2 - - - -
1177A LYS* 1.3 75.9 - - - +
1179A VAL* 1.3 57.2 + - - +
1181A ASP* 3.8 5.9 - - - +
1182A PHE* 3.1 26.3 + - - +
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Residues in contact with VAL1179 (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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1038A ILE* 3.9 10.8 - - + -
1047A MET* 4.8 0.7 - - + -
1063A TRP* 3.7 28.7 - - + +
1065A ASN* 5.5 2.7 - - - +
1108A LEU* 3.8 28.3 - - + -
1111A ALA* 5.7 1.6 - - + -
1147A TRP* 3.9 23.6 - - + -
1175A GLU 3.6 13.7 - - - +
1176A VAL* 3.0 7.3 + - - +
1178A SER* 1.3 71.3 - - - +
1180A VAL* 1.3 66.2 + - - +
1181A ASP 3.1 1.8 - - - -
1182A PHE* 3.2 2.3 + - - +
1183A ILE* 3.0 40.8 + - + +
1192A PHE* 4.5 1.3 - - + -
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Residues in contact with VAL1180 (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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1147A TRP* 3.5 29.6 - - + -
1171A ASN* 3.7 32.8 - - - +
1176A VAL* 2.8 23.2 + - + +
1177A LYS* 3.6 11.0 - - + +
1179A VAL* 1.3 71.6 - - - +
1181A ASP* 1.3 67.9 + - - +
1184A GLN* 3.0 53.4 + - - +
1257A TRP* 3.7 23.2 - - + +
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Residues in contact with ASP1181 (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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1038A ILE 6.1 0.2 - - - +
1177A LYS* 2.7 55.7 + - - +
1178A SER* 3.8 6.6 + - - +
1180A VAL* 1.3 77.8 - - - +
1182A PHE* 1.3 66.9 + - - +
1184A GLN* 4.1 4.0 + - - +
1185A LYS* 3.0 27.0 + - - +
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Residues in contact with PHE1182 (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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1036A VAL* 4.5 13.9 - - + -
1038A ILE* 3.6 34.8 - - + +
1051A LYS* 6.1 0.2 - - - -
1063A TRP* 3.8 16.8 - + + -
1106A PHE* 3.4 44.9 - + - -
1178A SER 3.1 18.6 + - - +
1179A VAL* 3.2 6.0 + - - +
1181A ASP* 1.3 77.2 - - - +
1183A ILE* 1.3 57.9 + - - +
1185A LYS* 3.2 37.7 - - - +
1186A HIS* 2.9 30.9 + + + +
1189A PHE* 4.2 14.1 - + - -
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Residues in contact with ILE1183 (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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1063A TRP* 3.9 21.8 - - + -
1179A VAL* 3.0 28.8 + - + +
1182A PHE* 1.3 77.1 - - - +
1184A GLN* 1.3 59.9 + - + +
1186A HIS* 3.2 4.3 + - - +
1187A GLY* 2.9 26.0 + - - -
1189A PHE* 4.0 29.4 + - + -
1192A PHE* 3.7 35.9 - - + -
1257A TRP* 3.6 24.5 - - + -
1261A ASN* 6.1 0.7 - - + -
1263A ILE* 3.9 19.7 - - + -
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Residues in contact with GLN1184 (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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1177A LYS* 6.1 0.2 - - - +
1180A VAL* 3.0 37.2 + - - +
1181A ASP* 4.3 4.8 + - - +
1183A ILE* 1.3 74.3 - - + +
1185A LYS* 1.3 66.0 + - - +
1187A GLY* 3.7 11.4 + - - +
1257A TRP* 3.9 14.9 - - + +
1261A ASN* 3.2 25.6 + - + +
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Residues in contact with LYS1185 (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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1058A ARG* 5.4 0.9 + - - -
1181A ASP 3.0 18.5 + - - +
1182A PHE* 3.2 47.6 - - - +
1184A GLN* 1.3 76.1 - - - +
1186A HIS* 1.3 85.8 + - - +
1187A GLY* 4.4 0.5 - - - -
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Residues in contact with HIS1186 (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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1051A LYS* 6.2 0.7 - - - -
1058A ARG* 3.2 53.2 + - + +
1059A ARG 3.2 28.7 + - - -
1061A ALA* 3.7 13.8 - - + +
1104A ASP* 5.1 1.8 + - - -
1106A PHE* 4.1 19.1 - + - -
1182A PHE* 2.9 17.5 + + + +
1183A ILE 3.4 8.1 - - - +
1185A LYS* 1.3 90.0 - - - +
1187A GLY* 1.3 56.1 + - - +
1188A ASN* 3.1 35.9 + - + -
1189A PHE* 3.4 21.5 - + + -
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Residues in contact with GLY1187 (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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1183A ILE 2.9 14.4 + - - -
1184A GLN* 3.9 11.7 - - - -
1185A LYS 3.4 0.6 - - - -
1186A HIS* 1.3 74.9 - - - +
1188A ASN* 1.3 60.1 + - - +
1189A PHE 3.8 2.4 + - - -
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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