Contacts of the helix formed by residues 1245 - 1262 (chain A) in PDB entry 3AVS
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 THR1245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957A HIS* 6.3 0.9 - - + +
961A THR* 5.5 8.7 - - + +
1118A LEU* 5.5 0.9 - - - +
1243A PRO* 2.9 24.1 + - + +
1244A LEU* 1.3 80.9 - - - +
1246A ALA* 1.3 64.8 + - - +
1247A CYS* 3.6 9.2 + - - +
1248A GLN* 3.1 23.6 + - - +
1249A TYR* 3.1 22.3 + - - +
1285A ASP* 5.8 0.4 - - - -
1288A LEU* 3.9 8.2 - - - +
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Residues in contact with ALA1246 (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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1245A THR* 1.3 73.6 - - - +
1247A CYS* 1.3 57.0 + - - +
1249A TYR 3.4 0.2 + - - -
1250A LYS* 2.9 34.3 + - - +
1285A ASP* 4.1 7.8 + - - +
1287A LYS* 3.8 40.2 - - + -
1288A LEU* 3.9 26.9 - - - +
1291A MET* 3.5 8.4 - - + +
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Residues in contact with CYS1247 (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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961A THR 5.8 2.2 - - - +
963A PRO* 4.4 27.6 - - + -
1222A ALA* 5.3 3.4 - - - -
1245A THR* 3.1 8.4 - - - +
1246A ALA* 1.3 80.5 - - - +
1248A GLN* 1.3 63.4 + - - +
1250A LYS* 3.7 6.7 - - - +
1251A LEU* 3.1 41.8 + - - +
1287A LYS* 6.1 1.1 - - - +
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Residues in contact with GLN1248 (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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1118A LEU* 4.0 9.4 - - + -
1150A ASN 4.4 2.8 + - - -
1151A ASN 3.0 27.7 + - - -
1152A PHE* 3.5 12.5 - - + +
1153A CYS* 3.2 25.9 + - - -
1222A ALA* 3.7 13.2 - - + +
1242A GLY* 3.5 12.0 - - - -
1243A PRO* 3.5 38.0 - - + +
1245A THR* 3.1 16.6 + - - +
1247A CYS* 1.3 75.7 - - - +
1249A TYR* 1.3 66.6 + - - +
1251A LEU* 3.4 1.5 + - - +
1252A ALA* 3.0 18.1 + - - +
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Residues in contact with TYR1249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A LEU* 4.7 9.8 - - + +
1245A THR 3.1 7.9 + - - +
1246A ALA 4.0 1.1 - - - +
1248A GLN* 1.3 78.5 - - - +
1250A LYS* 1.3 57.5 + - - +
1252A ALA* 3.2 5.3 + - - +
1253A VAL* 2.9 50.7 + - + +
1270A MET* 3.9 18.6 - - + -
1274A SER* 2.7 31.3 + - - -
1277A MET* 3.7 29.8 - - + -
1288A LEU* 3.6 24.2 - - + -
1291A MET* 3.7 42.2 - - + -
1292A ILE* 3.7 9.9 - - + -
1295A CYS* 3.3 20.8 - - + +
1512A EDO 4.5 3.1 - - - -
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Residues in contact with LYS1250 (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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1246A ALA 2.9 18.9 + - - +
1247A CYS* 3.7 6.7 - - - +
1249A TYR* 1.3 78.1 - - - +
1251A LEU* 1.3 59.3 + - + +
1253A VAL* 3.3 2.9 + - - +
1254A GLU* 2.9 57.1 + - - +
1287A LYS* 4.4 15.8 - - - +
1291A MET* 3.8 20.1 - - + +
1512A EDO 3.8 26.8 - - - +
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Residues in contact with LEU1251 (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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1151A ASN* 3.2 34.6 + - + +
1171A GLU* 3.6 32.1 - - + +
1222A ALA* 3.6 37.5 - - + +
1247A CYS* 3.1 32.1 + - - +
1248A GLN* 3.9 5.2 - - - +
1250A LYS* 1.3 81.3 - - + +
1252A ALA* 1.3 62.5 + - - +
1254A GLU* 3.7 18.9 - - - +
1255A ARG* 3.1 18.7 + - - +
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Residues in contact with ALA1252 (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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1150A ASN* 3.2 29.3 + - - +
1151A ASN* 4.5 0.2 - - - +
1152A PHE* 3.8 18.4 - - + -
1248A GLN* 3.0 18.6 + - - +
1249A TYR* 3.2 5.6 + - - +
1251A LEU* 1.3 76.7 - - - +
1253A VAL* 1.3 59.2 + - - +
1255A ARG* 3.5 0.9 + - - +
1256A TYR* 3.0 27.6 + - - +
1270A MET* 3.7 22.5 - - + +
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Residues in contact with VAL1253 (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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1249A TYR* 2.9 51.6 + - + +
1250A LYS 3.8 3.4 - - - +
1252A ALA* 1.3 74.4 - - - +
1254A GLU* 1.3 64.7 + - - +
1256A TYR* 3.1 9.0 + - - +
1257A GLU* 2.9 27.6 + - + +
1270A MET* 4.1 9.0 - - + -
1295A CYS* 5.7 0.4 - - + -
1298A ARG* 4.4 7.0 - - - +
1508A EDO 3.5 34.8 - - - +
1512A EDO 3.9 21.8 - - - -
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Residues in contact with GLU1254 (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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921A PRO* 4.5 6.1 - - + +
1151A ASN* 5.6 1.1 - - - +
1171A GLU* 5.3 0.5 - - - +
1250A LYS* 2.9 51.6 + - - +
1251A LEU* 3.7 23.6 - - - +
1252A ALA 3.3 0.2 - - - -
1253A VAL* 1.3 77.2 - - - +
1255A ARG* 1.3 56.2 + - - +
1257A GLU* 3.2 6.9 + - - +
1258A TRP* 2.9 29.1 + - - +
1512A EDO 4.4 10.7 + - - -
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Residues in contact with ARG1255 (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 GLN* 2.9 42.2 + - - +
1148A GLU 5.0 2.4 + - - -
1150A ASN* 3.7 29.8 - - - +
1151A ASN* 3.6 21.3 + - - +
1174A TRP* 3.5 35.8 - - - +
1189A LEU* 3.6 22.0 - - - +
1251A LEU 3.1 16.8 + - - +
1252A ALA 4.0 0.2 - - - +
1254A GLU* 1.3 74.4 - - - +
1256A TYR* 1.3 60.0 + - - +
1258A TRP* 3.8 16.2 - - - +
1259A ASN* 2.8 59.0 + - - +
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Residues in contact with TYR1256 (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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1150A ASN* 3.6 2.9 + - - +
1252A ALA 3.0 15.9 + - - +
1253A VAL* 3.2 9.4 - - - +
1255A ARG* 1.3 78.3 - - - +
1257A GLU* 1.3 73.5 + - - +
1259A ASN* 3.5 3.3 + - - +
1260A LYS* 3.2 48.5 + - + +
1266A SER* 3.4 33.0 + - - -
1268A VAL 4.2 0.7 - - - -
1269A PRO* 4.6 0.4 - - + -
1270A MET* 3.5 28.3 - - + -
1271A VAL* 3.5 14.0 - - + +
1330A TYR* 6.0 0.2 - + - -
1336A VAL* 5.3 0.3 - - - +
1337A GLU* 2.7 49.4 + - + +
1508A EDO 3.8 24.7 - - - -
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Residues in contact with GLU1257 (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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921A PRO* 3.7 24.7 - - + +
1253A VAL* 2.9 20.4 + - + +
1254A GLU* 3.2 8.9 + - - +
1256A TYR* 1.3 82.7 - - - +
1258A TRP* 1.3 66.1 + - - +
1260A LYS* 3.2 33.4 + - - +
1261A LEU* 3.2 9.9 + - - +
1298A ARG* 4.5 5.1 + - - +
1508A EDO 3.0 33.3 + - - +
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Residues in contact with TRP1258 (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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921A PRO* 3.3 43.2 - - + +
922A ARG* 3.7 9.4 - - + -
923A PRO* 3.6 27.6 - - + -
1174A TRP* 3.8 25.4 - + + -
1178A ASN* 5.1 7.7 + - - -
1188A PHE* 5.7 0.2 - - - -
1189A LEU* 3.8 21.1 - - + +
1254A GLU 2.9 17.9 + - - +
1255A ARG* 3.8 26.2 - - - +
1257A GLU* 1.3 72.7 - - - +
1259A ASN* 1.3 67.1 + - - +
1261A LEU* 3.1 11.7 + - + +
1262A GLN* 3.0 62.8 + - + +
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Residues in contact with ASN1259 (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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1150A ASN* 4.2 6.1 + - - +
1189A LEU* 3.7 17.5 - - - +
1255A ARG* 2.8 46.1 + - - +
1256A TYR 3.6 0.9 - - - +
1258A TRP* 1.3 77.3 - - - +
1260A LYS* 1.3 62.3 + - - +
1262A GLN* 3.0 3.0 + - - -
1263A SER 2.9 19.6 + - - -
1264A VAL* 2.9 40.4 + - - +
1265A LYS 4.0 3.6 + - - -
1266A SER* 3.0 34.3 + - - +
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Residues in contact with LYS1260 (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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1256A TYR* 3.2 44.3 + - + +
1257A GLU* 3.2 29.9 + - - +
1259A ASN* 1.3 77.3 - - - +
1261A LEU* 1.3 62.5 + - - +
1263A SER* 3.2 15.7 + - - +
1264A VAL 5.0 1.3 - - - -
1336A VAL* 3.7 35.0 - - + +
1337A GLU 5.8 0.2 + - - -
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Residues in contact with LEU1261 (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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920A PRO* 4.9 10.1 - - + -
921A PRO* 3.8 33.0 - - + +
1257A GLU 3.2 7.5 + - - +
1258A TRP* 3.1 23.1 + - + +
1260A LYS* 1.3 79.7 - - - +
1262A GLN* 1.3 69.7 + - - +
1263A SER* 3.3 2.8 + - - -
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Residues in contact with GLN1262 (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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1187A ASN* 5.6 3.5 + - - -
1189A LEU* 4.1 8.3 - - + -
1258A TRP* 3.0 64.3 + - + +
1259A ASN 3.0 5.6 + - - +
1261A LEU* 1.3 88.8 + - - +
1263A SER* 1.3 70.9 + - - +
1264A VAL* 3.1 19.8 + - + +
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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
------------------------------------------------------------
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