Contacts of the helix formed by residues 1246 - 1261 (chain A) in PDB entry 5G04
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 PRO1246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1200A GLY 5.6 2.0 - - - +
1202A GLU* 4.7 16.6 - - + +
1231A HIS* 6.5 0.2 - - + -
1244A ASP 4.0 5.2 - - - +
1245A VAL* 1.4 92.1 - - + +
1247A HIS* 1.3 56.2 + - - +
1248A ASN* 4.6 2.9 - - + +
1249A VAL* 2.6 52.1 + - + +
112R HIS* 5.4 11.7 - - + +
116R TRP* 5.1 5.6 - - + -
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Residues in contact with HIS1247 (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 VAL 3.6 3.4 + - - -
1246A PRO* 1.3 67.2 - - - +
1248A ASN* 1.3 57.8 + - - +
1249A VAL 2.7 12.3 + - - -
1250A GLN* 2.8 34.0 + - - +
1251A VAL* 3.7 13.5 + - + +
1287A TYR* 3.4 47.2 + + - +
1289A THR* 3.5 27.1 + - - +
1290A ASP* 3.8 14.4 + - - +
1291A ARG* 4.3 2.0 - - - -
1293A SER* 4.5 1.4 + - - -
1294A TYR* 3.2 38.1 - + + +
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Residues in contact with ASN1248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A TRP* 4.0 22.0 - - - +
1202A GLU* 3.2 32.8 + - - +
1206A ILE* 3.5 13.2 - - - +
1246A PRO* 3.2 3.2 + - + +
1247A HIS* 1.3 79.6 + - - +
1249A VAL* 1.3 60.0 + - - +
1251A VAL* 3.3 18.2 - - - +
1599A ASN* 4.0 15.1 + - - +
1603A LEU* 3.9 17.7 - - - +
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Residues in contact with VAL1249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A GLU* 3.4 34.5 - - + +
1205A SER* 3.9 25.8 - - - +
1206A ILE* 4.2 4.0 - - - -
1209A LEU* 4.0 19.6 - - + +
1231A HIS* 4.1 17.3 - - + -
1245A VAL* 4.2 5.2 - - + -
1246A PRO* 2.6 39.0 + - + +
1248A ASN* 1.3 71.9 - - - +
1250A GLN* 1.3 62.4 + - - +
1252A ALA* 3.2 21.1 + - - +
1253A ALA* 3.5 4.7 + - - +
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Residues in contact with GLN1250 (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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1231A HIS* 4.1 2.4 + - - +
1232A ILE* 3.7 14.3 - - + +
1233A PRO* 3.5 26.0 - - - +
1243A LEU* 5.4 1.8 + - - +
1245A VAL* 3.5 37.9 + - + +
1246A PRO 3.7 2.0 - - - +
1247A HIS* 2.8 40.3 + - - +
1249A VAL* 1.3 69.9 - - - +
1251A VAL* 1.3 53.6 + - - +
1253A ALA* 3.1 10.2 + - - +
1254A VAL* 2.6 39.1 + - - +
1287A TYR* 3.9 9.8 - - - -
1294A TYR* 3.3 26.3 - - + -
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Residues in contact with VAL1251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247A HIS* 3.7 12.3 + - + +
1248A ASN* 3.3 25.6 - - - +
1250A GLN* 1.3 74.8 - - - +
1252A ALA* 1.3 67.0 + - - +
1254A VAL* 3.3 11.1 - - - +
1255A VAL* 2.9 32.9 + - - +
1293A SER* 3.9 10.5 - - - +
1294A TYR* 3.5 42.1 - - + +
1297A ALA* 3.4 12.2 - - + +
1603A LEU* 3.5 30.1 - - + -
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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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1206A ILE* 4.2 20.0 - - + +
1209A LEU* 4.9 5.6 - - + -
1210A LEU* 3.4 30.5 - - + +
1249A VAL 3.2 11.6 + - - +
1250A GLN 3.2 0.6 - - - -
1251A VAL* 1.3 78.3 - - + +
1253A ALA* 1.3 55.4 + - - +
1255A VAL* 3.0 9.5 + - - +
1256A GLY* 2.4 32.6 + - - -
1603A LEU* 4.1 15.0 - - + -
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Residues in contact with ALA1253 (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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1209A LEU* 3.7 27.9 - - + +
1228A LEU* 4.1 18.0 - - + +
1231A HIS* 4.2 9.6 - - + -
1232A ILE* 3.7 16.6 - - + -
1249A VAL 3.5 3.6 + - - +
1250A GLN 3.1 7.5 + - - +
1252A ALA* 1.3 73.4 - - - +
1254A VAL* 1.3 55.7 + - - +
1256A GLY* 3.7 4.7 - - - +
1257A ILE* 2.4 40.6 + - - +
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Residues in contact with VAL1254 (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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1232A ILE* 3.5 15.4 - - + +
1250A GLN 2.6 25.9 + - - +
1251A VAL* 3.3 9.9 - - - +
1253A ALA* 1.3 74.7 - - - +
1255A VAL* 1.3 56.9 + - - +
1257A ILE* 2.9 18.0 + - - +
1258A GLY 3.3 7.1 + - - -
1273A LEU* 4.3 9.9 - - + -
1276A GLU* 3.6 14.8 - - - +
1294A TYR* 3.5 33.4 - - + +
1297A ALA* 3.9 1.8 - - + +
1298A ALA* 3.4 37.2 - - + +
1301A ALA* 3.4 8.7 - - + +
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Residues in contact with VAL1255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A LEU* 3.9 8.5 - - + -
1251A VAL 2.9 27.0 + - - +
1252A ALA* 3.3 6.5 - - - +
1254A VAL* 1.3 69.2 - - - +
1256A GLY* 1.3 67.3 + - - +
1258A GLY* 3.1 9.9 + - - -
1259A LEU* 3.3 18.0 + - + +
1297A ALA* 3.7 19.3 - - + +
1300A LEU* 5.1 2.7 - - + -
1301A ALA* 4.2 7.2 - - - -
1304A MET* 3.7 24.4 - - + +
1586A CYS* 5.1 0.2 - - - -
1606A LEU* 3.4 46.4 - - + -
1609A LEU* 5.3 0.9 - - + -
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Residues in contact with GLY1256 (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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1209A LEU 5.0 0.2 - - - -
1210A LEU* 4.0 2.0 - - - +
1213A SER* 3.1 25.7 - - - -
1228A LEU* 3.6 7.0 - - - -
1252A ALA 2.4 23.1 + - - -
1253A ALA* 2.8 8.5 + - - -
1255A VAL* 1.3 68.5 - - - +
1257A ILE* 1.3 62.6 + - - +
1258A GLY 3.1 0.9 + - - -
1259A LEU* 3.1 16.7 + - - +
1260A VAL* 3.1 14.9 + - - +
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Residues in contact with ILE1257 (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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1225A THR* 4.9 3.1 - - - +
1228A LEU* 3.5 23.1 - - + -
1232A ILE* 5.0 4.5 - - + -
1235A LEU* 3.6 38.1 - - + -
1253A ALA 2.4 26.7 + - - +
1254A VAL* 2.9 12.7 + - - +
1256A GLY* 1.3 67.0 - - - +
1258A GLY* 1.3 57.9 + - - +
1260A VAL* 3.1 5.4 + - + +
1261A TYR* 3.0 55.5 + - + +
1269A THR* 3.9 27.4 - - + +
1272A VAL* 6.2 0.4 - - + -
1273A LEU* 4.1 18.6 - - + -
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Residues in contact with GLY1258 (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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1254A VAL 3.3 6.3 + - - -
1255A VAL 3.1 7.3 + - - -
1256A GLY 3.0 1.2 - - - -
1257A ILE* 1.3 78.8 - - - +
1259A LEU* 1.3 55.9 + - - +
1261A TYR 3.4 1.4 + - - -
1262A GLN* 2.9 30.7 + - - +
1301A ALA* 3.6 31.4 - - - -
1304A MET* 3.7 12.0 - - - +
1305A VAL* 4.1 5.1 - - - +
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Residues in contact with LEU1259 (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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1210A LEU* 4.0 18.8 - - + +
1213A SER* 3.5 32.8 - - - +
1214A ALA* 4.2 7.6 - - + +
1217A LEU* 3.0 24.3 - - + -
1218A GLY* 2.3 35.3 + - - -
1255A VAL* 3.3 19.5 + - + +
1256A GLY* 3.4 6.1 - - - +
1258A GLY* 1.3 77.2 - - - +
1260A VAL* 1.3 50.0 + - - +
1262A GLN* 3.2 16.5 + - - +
1304A MET* 4.5 7.4 - - - -
1609A LEU* 3.7 30.1 - - + -
1612A LEU* 3.8 9.4 - - + -
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Residues in contact with VAL1260 (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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1213A SER* 4.1 13.5 - - - -
1216A LYS* 4.2 6.7 - - + -
1217A LEU 4.8 1.3 - - - +
1218A GLY* 3.2 17.0 - - - +
1220A MET* 3.2 26.4 + - - +
1221A ASP 4.7 3.1 - - - +
1224A ILE* 3.8 22.0 - - + -
1225A THR* 3.9 21.5 - - - +
1228A LEU* 3.6 19.3 - - + -
1256A GLY 3.1 15.8 + - - +
1257A ILE* 3.1 12.1 + - + +
1259A LEU* 1.3 75.4 - - - +
1261A TYR* 1.3 72.3 + - + +
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Residues in contact with TYR1261 (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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1220A MET* 3.6 48.0 - - + -
1225A THR* 2.6 35.4 + - + +
1235A LEU* 4.9 3.8 - - + +
1257A ILE* 3.0 46.4 + - + +
1258A GLY 3.6 1.8 - - - -
1260A VAL* 1.3 84.4 - - + +
1262A GLN* 1.3 57.0 + - - +
1263A GLY 3.3 0.3 + - - -
1264A THR* 2.5 37.7 + - - +
1266A HIS* 4.2 16.5 + + + -
1269A THR* 3.5 24.0 - - + -
1305A VAL* 3.6 27.7 - - + -
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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