Contacts of the helix formed by residues 1173 - 1184 (chain A) in PDB entry 3AVR
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 TYR1173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926A SER* 4.4 6.1 - - - -
927A PRO* 3.5 39.9 + - + +
929A PRO 4.9 2.6 + - - -
930A PRO* 5.5 0.5 - - - +
931A LEU* 3.4 30.0 + - + +
1169A VAL* 3.5 21.8 - - + -
1170A PRO* 3.0 25.0 + - + -
1172A GLY* 1.3 78.8 - - - +
1174A TRP* 1.3 63.7 + - - +
1175A GLY 3.2 3.4 - - - -
1176A VAL* 3.1 20.0 + - + +
1177A LEU* 3.1 13.0 + - - +
1204A ASN 3.8 12.7 + - - -
1205A VAL* 4.1 20.2 - - + -
1206A PRO* 3.3 32.5 - - + +
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Residues in contact with TRP1174 (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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922A ARG 4.0 5.6 - - - -
923A PRO* 3.7 25.4 - - + -
924A PRO* 3.1 32.9 - - + +
1147A GLN* 3.5 24.5 - - - +
1170A PRO 4.1 0.8 + - - -
1171A GLU* 3.0 44.3 + - - +
1172A GLY 3.3 0.8 - - - -
1173A TYR* 1.3 77.9 - - - +
1175A GLY* 1.3 55.4 + - - +
1177A LEU* 3.3 4.7 + - - +
1178A ASN* 2.8 34.4 + - + +
1188A PHE* 3.6 28.3 - + + -
1225A VAL* 3.9 14.1 - - + -
1254A GLU* 5.9 0.8 + - - -
1255A ARG* 3.5 22.8 - - - +
1258A TRP* 3.6 35.9 - + + -
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Residues in contact with GLY1175 (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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923A PRO* 3.9 20.3 - - - +
924A PRO* 3.3 29.2 - - - +
1172A GLY 4.7 0.2 + - - -
1173A TYR 3.2 0.8 - - - -
1174A TRP* 1.3 82.6 - - - +
1176A VAL* 1.3 56.5 + - - +
1178A ASN* 3.3 4.0 + - - +
1179A ASP* 3.0 34.3 + - - -
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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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924A PRO 4.2 0.4 + - - -
925A SER 4.7 0.4 - - - -
926A SER* 3.6 43.3 - - - +
927A PRO* 4.4 1.3 - - + -
1172A GLY 5.6 0.2 - - - +
1173A TYR* 3.1 20.3 + - + +
1175A GLY* 1.3 77.0 - - - +
1177A LEU* 1.3 62.5 + - + +
1179A ASP* 3.2 10.2 + - + +
1180A PHE* 3.0 35.7 + - + -
1203A ALA* 4.6 6.7 - - + +
1205A VAL* 3.7 27.6 - - + -
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Residues in contact with LEU1177 (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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1021A TRP* 4.7 4.6 - - + -
1169A VAL* 4.1 13.2 - - + -
1173A TYR 3.1 15.0 + - - +
1174A TRP 3.7 7.2 - - - +
1176A VAL* 1.3 75.7 - - - +
1178A ASN* 1.3 66.4 + - - +
1180A PHE* 3.2 8.0 + - + +
1181A CYS* 2.9 26.2 + - - -
1188A PHE* 3.9 12.1 - - + -
1193A TRP* 4.4 13.0 - - + -
1195A PRO* 5.5 0.2 - - + -
1200A LEU* 3.8 30.5 - - + -
1205A VAL* 4.3 17.5 - - + -
1225A VAL* 3.3 41.3 - - + -
1227A TRP* 4.5 9.0 - - + -
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Residues in contact with ASN1178 (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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923A PRO* 3.8 23.6 - - - +
1174A TRP* 2.8 25.1 + - + +
1175A GLY* 3.4 11.4 - - - +
1176A VAL 3.2 0.2 - - - -
1177A LEU* 1.3 76.4 - - - +
1179A ASP* 1.3 73.5 + - - +
1181A CYS* 3.2 4.5 + - - +
1182A GLU* 3.0 37.2 + - - +
1188A PHE* 3.2 35.4 - - + +
1189A LEU* 6.0 0.2 - - - +
1258A TRP* 5.1 7.4 + - - -
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Residues in contact with ASP1179 (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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923A PRO* 5.7 1.6 - - - +
924A PRO 5.5 1.0 - - - +
925A SER* 6.2 0.3 - - - -
1175A GLY 3.0 20.6 + - - +
1176A VAL* 3.5 11.1 - - - +
1177A LEU 3.2 0.2 - - - -
1178A ASN* 1.3 84.2 + - - +
1180A PHE* 1.3 65.6 + - - +
1182A GLU* 3.3 7.0 + - - +
1183A LYS* 2.9 40.0 + - + +
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Residues in contact with PHE1180 (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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1021A TRP* 3.4 30.3 - + + -
1176A VAL* 3.0 34.4 + - + -
1177A LEU* 3.2 6.7 + - - +
1179A ASP* 1.3 75.2 - - - +
1181A CYS* 1.3 63.5 + - - +
1183A LYS* 3.3 10.0 + - + +
1184A ASN* 3.0 35.9 + - - -
1199A ASP* 3.4 40.4 - - + -
1200A LEU* 3.7 27.4 - - + -
1203A ALA* 3.6 22.4 - - + -
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Residues in contact with CYS1181 (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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1021A TRP* 4.4 7.0 - - - -
1177A LEU 2.9 17.2 + - - -
1178A ASN 3.4 8.1 - - - +
1180A PHE* 1.3 76.4 - - - +
1182A GLU* 1.3 59.0 + - + +
1184A ASN* 2.8 20.3 + - - -
1185A ASN 3.1 0.2 + - - -
1186A LEU* 2.9 36.9 + - + +
1188A PHE* 3.9 17.9 - - - +
1193A TRP* 3.5 52.0 - - - -
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Residues in contact with GLU1182 (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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1178A ASN* 3.0 33.3 + - - +
1179A ASP* 3.7 10.5 - - - +
1181A CYS* 1.3 76.1 - - + +
1183A LYS* 1.3 60.2 + - + +
1185A ASN* 3.0 19.6 + - - -
1186A LEU 3.6 13.9 + - - +
1187A ASN* 4.7 11.8 + - - -
1188A PHE 4.9 1.6 + - - -
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Residues in contact with LYS1183 (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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1179A ASP* 2.9 29.4 + - + +
1180A PHE* 3.7 13.5 - - + +
1181A CYS 3.2 0.2 - - - -
1182A GLU* 1.3 77.6 - - + +
1184A ASN* 1.3 63.2 + - - +
1185A ASN* 3.3 1.1 + - - +
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Residues in contact with ASN1184 (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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1020A ILE* 5.6 0.9 - - - -
1021A TRP* 3.7 40.3 + - + +
1180A PHE* 3.0 31.6 + - - +
1181A CYS 2.8 6.6 + - - +
1183A LYS* 1.3 83.3 - - - +
1185A ASN* 1.3 68.5 + - - +
1186A LEU* 3.3 23.0 + - + +
1199A ASP* 4.9 2.0 + - - -
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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