Contacts of the helix formed by residues 1246 - 1259 (chain A) in PDB entry 4YOC
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 SER1246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ALA* 4.1 0.2 - - - +
1225A PRO 5.3 0.2 - - - -
1229A PHE* 3.4 33.4 - - - -
1242A LYS 3.3 7.0 + - - -
1243A PHE* 2.7 30.9 + - - -
1244A LYS 3.5 0.6 - - - -
1245A ASN* 1.3 84.0 - - - +
1247A LEU* 1.3 64.2 + - - +
1248A VAL* 3.1 10.1 + - - +
1249A VAL* 3.4 8.9 + - - +
1250A SER* 3.2 20.2 + - - -
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Residues in contact with LEU1247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145A PHE* 3.8 22.4 - - + -
1190A ASP* 5.2 4.5 - - - +
1191A CYS* 3.7 28.9 - - - -
1192A ASN* 4.5 9.0 - - - +
1224A PRO* 4.0 2.4 - - + +
1225A PRO* 3.7 42.2 + - + +
1245A ASN 5.7 0.4 - - - +
1246A SER* 1.3 73.2 - - - +
1248A VAL* 1.3 61.0 + - - +
1250A SER* 3.6 8.9 - - - +
1251A PHE* 2.9 29.3 + - - +
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Residues in contact with VAL1248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A PRO* 3.9 22.4 - - + -
1225A PRO 4.4 4.5 - - - +
1226A CYS* 4.4 8.7 - - - -
1229A PHE* 4.0 29.4 - - + -
1243A PHE* 4.2 12.6 - - + -
1246A SER* 3.1 6.0 - - - +
1247A LEU* 1.3 77.9 - - - +
1249A VAL* 1.3 58.8 + - - +
1251A PHE* 3.3 3.5 + - - +
1252A LEU* 2.9 37.9 + - + +
1265A LEU* 4.4 15.5 - - + -
1271A PHE* 4.4 8.1 - - + -
1283A THR* 4.1 19.5 - - - +
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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
----------------------------------------------------------
618A ALA* 5.0 4.7 - - + -
620A THR* 4.9 9.9 - - - +
624A VAL* 3.7 21.0 - - + +
625A TYR* 6.0 1.3 - - - -
628A PHE* 3.9 29.8 - - + -
1243A PHE* 3.2 27.6 - - + +
1244A LYS 3.6 19.3 - - - +
1245A ASN 4.9 0.4 - - - -
1246A SER* 3.4 9.1 + - - +
1248A VAL* 1.3 75.1 - - + +
1250A SER* 1.3 55.9 + - - +
1252A LEU* 3.5 8.7 + - - +
1253A SER* 2.6 40.7 + - - +
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Residues in contact with SER1250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.5 7.4 - - - +
619A THR 4.2 6.3 - - - -
1191A CYS* 4.1 16.8 - - - -
1192A ASN* 2.7 32.2 + - - -
1195A LEU* 4.2 0.6 - - - +
1246A SER 3.2 12.8 + - - -
1247A LEU* 3.6 13.0 - - - -
1248A VAL 3.3 0.2 - - - -
1249A VAL* 1.3 78.5 - - - +
1251A PHE* 1.3 56.3 + - - +
1253A SER* 3.1 8.5 + - - -
1254A TYR* 2.9 36.5 + - - -
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Residues in contact with PHE1251 (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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1144A VAL* 3.7 33.7 - - + -
1145A PHE* 4.2 12.5 - + + -
1220A LEU* 3.6 22.6 - - + +
1221A CYS* 3.5 6.1 - - - -
1222A GLY* 3.4 26.7 - - - -
1224A PRO* 4.3 6.1 - - + -
1247A LEU 2.9 18.4 + - - +
1248A VAL* 3.3 6.0 + - - +
1250A SER* 1.3 75.6 - - - +
1252A LEU* 1.3 56.9 + - - +
1254A TYR* 3.0 12.6 + - + +
1255A CYS* 2.9 25.5 + - - +
1263A PHE* 3.4 30.5 - + - -
1264A LEU 3.6 11.7 - - - -
1265A LEU* 3.6 29.8 - - + -
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Residues in contact with LEU1252 (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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624A VAL* 4.4 2.9 - - + -
628A PHE* 4.0 22.4 - - + -
1248A VAL* 2.9 27.3 + - + +
1249A VAL* 3.8 4.9 - - - +
1251A PHE* 1.3 75.8 - - - +
1253A SER* 1.3 57.0 + - - +
1255A CYS* 3.2 4.4 + - + +
1256A ASP* 2.9 23.4 + - - +
1263A PHE* 4.1 20.6 - - + -
1265A LEU* 4.9 2.7 - - + -
1283A THR* 3.9 46.0 - - + +
1286A CYS* 4.3 11.0 - - + -
1287A LEU* 4.1 19.7 - - + -
1290A MET* 3.2 22.7 - - + +
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Residues in contact with SER1253 (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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619A THR 3.6 8.2 + - - -
620A THR* 3.5 26.3 + - - -
621A THR* 3.9 10.0 + - - +
624A VAL* 4.0 13.3 - - - +
1195A LEU* 3.8 16.4 - - - -
1249A VAL 2.6 20.0 + - - -
1250A SER 3.1 9.2 + - - -
1252A LEU* 1.3 74.8 - - - +
1254A TYR* 1.3 60.7 + - - +
1256A ASP* 3.3 2.5 + - - +
1257A TYR* 2.9 31.7 + - - +
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Residues in contact with TYR1254 (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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1142A LEU* 4.1 13.5 - - + -
1144A VAL* 4.8 9.6 - - + -
1167A ILE* 3.7 25.0 - - + +
1191A CYS* 2.5 52.4 + - + +
1192A ASN* 5.4 0.2 - - - -
1194A LEU* 3.7 5.0 - - + +
1195A LEU* 3.4 31.8 + - + +
1198A VAL* 6.3 0.4 - - + -
1212A PRO* 6.1 1.1 - - + -
1220A LEU* 4.0 13.5 - - + -
1250A SER* 2.9 30.1 + - - -
1251A PHE* 3.2 13.2 - - + +
1253A SER* 1.3 76.5 - - - +
1255A CYS* 1.3 55.5 + - - +
1257A TYR* 4.7 1.1 - - - -
1258A TYR* 2.9 65.8 + + - +
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Residues in contact with CYS1255 (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 LEU* 3.6 8.4 - - - +
1251A PHE 2.9 7.7 + - - +
1252A LEU* 3.3 11.4 - - - +
1253A SER 3.2 0.2 - - - -
1254A TYR* 1.3 76.8 - - - +
1256A ASP* 1.3 57.2 + - - +
1259A ARG* 2.9 31.0 + - - -
1260A PRO* 3.6 4.8 - - - +
1263A PHE* 3.5 46.0 - - + -
1287A LEU* 4.0 11.0 - - - -
1290A MET* 4.0 2.5 - - + -
1292A TYR* 3.6 31.5 + - - -
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Residues in contact with ASP1256 (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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621A THR* 2.8 31.8 + - - +
623A LEU* 3.5 20.9 - - - +
624A VAL* 4.1 1.3 - - + -
847A GLY* 3.1 8.9 - - - -
848A GLY 4.3 3.8 + - - -
1252A LEU 2.9 16.3 + - - +
1253A SER 3.3 4.0 + - - +
1255A CYS* 1.3 75.0 - - - +
1257A TYR* 1.3 63.1 + - - +
1259A ARG* 2.7 57.2 + - - +
1290A MET* 3.6 28.1 - - + +
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Residues in contact with TYR1257 (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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621A THR* 4.4 6.5 - - + +
844A ALA 4.8 0.5 - - - +
847A GLY* 4.0 16.5 - - - -
848A GLY* 4.6 7.4 - - - +
1195A LEU* 4.4 14.8 - - + -
1198A VAL* 3.4 40.3 + - + +
1199A MET* 4.2 25.4 - - + -
1213A GLN* 4.5 5.7 + - - -
1214A LYS* 3.5 59.7 - - + +
1253A SER 2.9 17.9 + - - +
1254A TYR 3.9 1.8 - - - +
1256A ASP* 1.3 81.2 - - - +
1258A TYR* 1.3 89.0 + + - +
1259A ARG* 3.6 2.3 + - - +
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Residues in contact with TYR1258 (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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844A ALA 4.3 3.8 - - - +
1142A LEU* 4.3 9.0 - - + -
1195A LEU* 4.5 4.0 - - + -
1198A VAL* 3.7 15.0 - - + +
1212A PRO* 2.5 52.9 + - + +
1213A GLN* 3.7 19.3 - - - -
1214A LYS* 4.2 5.4 - - - +
1215A GLY 4.7 9.2 + - - -
1217A VAL* 3.6 37.7 - - + +
1220A LEU* 5.7 1.8 - - + -
1254A TYR* 2.9 54.7 + + - +
1257A TYR* 1.3 96.9 - + - +
1259A ARG* 1.3 72.2 + - - +
1260A PRO* 3.5 6.9 - - + -
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Residues in contact with ARG1259 (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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623A LEU* 4.6 10.5 - - - +
843A TRP* 2.7 71.9 + - + +
844A ALA* 3.4 36.4 - - - +
846A GLU* 3.6 15.8 + - - +
847A GLY* 3.6 16.2 - - - +
1217A VAL 4.7 1.0 - - - +
1255A CYS 2.9 11.4 + - - -
1256A ASP* 2.7 43.6 + - - +
1257A TYR 4.1 2.9 - - - +
1258A TYR* 1.3 80.3 - - - +
1260A PRO* 1.3 68.7 - - - +
1261A ARG* 5.6 0.2 - - - +
1290A MET* 4.1 14.0 + - - +
1292A TYR* 3.2 9.0 - - - -
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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