Contacts of the helix formed by residues 1247 - 1263 (chain A) in PDB entry 1MUK
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 GLY1247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1058A LEU* 5.1 6.2 - - - +
1208A ASN* 4.7 1.6 - - - -
1245A ILE* 3.4 2.8 - - - +
1246A HIS* 1.3 88.3 + - - +
1248A GLY* 1.3 61.0 + - - +
1250A ARG* 5.7 0.2 - - - +
1251A SER* 2.7 34.2 + - - -
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Residues in contact with GLY1248 (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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1207A LEU 5.1 0.9 - - - -
1208A ASN* 3.6 22.5 + - - -
1245A ILE* 2.9 21.3 + - - +
1246A HIS 3.3 1.0 + - - -
1247A GLY* 1.3 79.6 - - - +
1249A GLY* 1.3 66.9 + - - -
1250A ARG* 3.2 4.0 + - - -
1252A LEU* 3.0 22.2 + - - +
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Residues in contact with GLY1249 (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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1207A LEU 5.1 1.4 + - - -
1208A ASN 3.2 14.5 + - - -
1210A ASP 4.0 16.7 + - - -
1212A PRO* 3.9 7.0 - - - -
1215A MET* 3.8 1.7 - - - +
1218A LEU* 3.5 18.5 - - - +
1245A ILE* 4.1 12.8 - - - +
1248A GLY* 1.3 67.9 - - - -
1250A ARG* 1.3 65.0 + - - +
1252A LEU* 4.2 1.8 - - - -
1253A GLY 3.0 18.5 + - - -
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Residues in contact with ARG1250 (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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1212A PRO* 3.6 22.8 - - + +
1215A MET* 3.7 21.2 - - + +
1248A GLY* 3.2 1.0 - - - -
1249A GLY* 1.3 75.9 - - - +
1251A SER* 1.3 65.1 + - - +
1253A GLY 3.3 2.1 + - - -
1254A GLN* 3.3 29.0 + - + +
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Residues in contact with SER1251 (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 LEU* 6.3 1.1 - - - -
1247A GLY* 2.7 34.5 + - - -
1248A GLY 3.3 1.2 + - - -
1250A ARG* 1.3 76.0 - - - +
1252A LEU* 1.3 66.3 + - - +
1254A GLN* 3.3 8.7 + - - +
1255A ARG* 3.0 23.8 + - - +
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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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1055A ALA* 3.5 30.7 - - + +
1058A LEU* 4.3 14.8 - - + -
1059A VAL* 3.9 16.4 - - + -
1218A LEU* 4.4 9.6 - - + -
1222A LEU* 4.6 7.4 - - + -
1245A ILE* 3.8 29.2 - - + -
1248A GLY 3.0 18.1 + - - +
1249A GLY 3.7 4.9 - - - +
1251A SER* 1.3 77.7 - - - +
1253A GLY* 1.3 62.9 + - - +
1255A ARG* 3.1 17.4 + - + +
1256A PHE* 3.1 41.9 + - + -
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Residues in contact with GLY1253 (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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1215A MET* 3.8 15.5 - - - -
1217A TRP* 3.5 22.2 - - - -
1218A LEU* 4.2 7.5 - - - +
1249A GLY 3.0 11.3 + - - -
1250A ARG 3.3 3.6 + - - -
1251A SER 3.3 0.2 - - - -
1252A LEU* 1.3 77.0 - - - +
1254A GLN* 1.3 56.1 + - - +
1256A PHE 3.1 2.6 + - - -
1257A MET* 2.8 33.2 + - - +
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Residues in contact with GLN1254 (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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1215A MET* 3.7 20.0 - - - +
1250A ARG* 3.3 24.2 + - + +
1251A SER* 3.7 8.7 - - - +
1253A GLY* 1.3 75.1 - - - +
1255A ARG* 1.3 57.6 + - - +
1257A MET* 2.9 20.4 + - - +
1258A THR* 2.8 35.5 + - - +
1261A ARG* 5.0 7.8 + - - -
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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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1051A LYS 5.2 2.7 + - - +
1054A GLU* 3.9 28.3 + - - +
1055A ALA* 4.2 21.8 - - + +
1058A LEU* 3.7 37.5 - - - +
1251A SER 3.0 15.2 + - - +
1252A LEU* 3.1 11.9 + - - +
1254A GLN* 1.3 79.2 - - - +
1256A PHE* 1.3 62.0 + - - +
1258A THR* 3.4 8.6 + - - +
1259A TRP* 3.3 16.8 + - - +
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Residues in contact with PHE1256 (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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1052A LEU* 4.0 18.2 - - + -
1055A ALA* 3.5 22.9 - - + -
1056A TYR* 3.6 33.2 - + - -
1176A VAL* 4.0 7.9 - - + -
1217A TRP* 4.0 2.2 - + + -
1218A LEU* 3.8 20.9 - - + -
1221A ILE* 3.9 24.5 - - + -
1222A LEU* 6.3 0.2 - - + -
1225A LEU* 5.6 1.6 - - + -
1252A LEU* 3.1 50.5 + - + -
1253A GLY 3.1 6.4 + - - +
1255A ARG* 1.3 72.5 - - - +
1257A MET* 1.3 60.6 + - - +
1259A TRP* 3.2 7.5 + - - +
1260A MET* 2.8 48.2 + - + +
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Residues in contact with MET1257 (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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1133A THR* 2.8 33.0 - - + +
1134A LEU* 3.4 36.1 - - + +
1215A MET* 4.8 5.8 - - - -
1217A TRP* 3.9 23.3 - - + +
1253A GLY 2.8 16.9 + - - +
1254A GLN* 2.9 29.8 + - - +
1256A PHE* 1.3 74.4 - - - +
1258A THR* 1.3 65.6 + - - +
1260A MET* 3.1 7.7 + - + +
1261A ARG* 3.0 41.4 + - - +
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Residues in contact with THR1258 (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* 5.2 7.4 - - + +
1254A GLN* 2.8 13.8 + - - +
1255A ARG* 3.6 11.4 - - - +
1257A MET* 1.3 76.5 - - - +
1259A TRP* 1.3 64.4 + - - +
1261A ARG* 3.4 19.7 + - - +
1262A GLN* 3.1 54.2 + - - +
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Residues in contact with TRP1259 (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* 4.1 30.2 - - + +
1052A LEU* 3.2 48.0 - - + +
1130A ARG* 4.9 4.5 - - - -
1175A VAL 3.6 22.9 - - - -
1176A VAL* 3.8 10.3 - - + -
1177A ASN* 3.0 34.3 - - - -
1255A ARG 3.3 8.5 + - - +
1256A PHE 3.2 8.2 + - - +
1257A MET 3.1 0.4 - - - -
1258A THR* 1.3 83.4 - - - +
1260A MET* 1.3 71.9 + - + +
1262A GLN* 3.3 13.5 + - + +
1263A GLU* 3.5 48.6 + - + +
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Residues in contact with MET1260 (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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1003A ILE* 4.3 3.1 - - - +
1004A HIS 5.3 0.3 + - - -
1130A ARG* 3.1 45.7 + - + +
1133A THR* 3.9 25.4 - - + -
1134A LEU* 4.1 15.3 - - + -
1175A VAL* 3.6 34.3 - - + +
1176A VAL* 5.4 1.3 - - + -
1217A TRP* 3.4 39.3 - - + -
1221A ILE* 5.2 0.7 - - + -
1256A PHE* 2.8 27.7 + - + +
1257A MET* 3.1 8.3 + - - +
1259A TRP* 1.3 85.5 - - + +
1261A ARG* 1.3 60.0 + - - +
1262A GLN 3.5 0.2 + - - -
1263A GLU* 4.0 4.3 + - - +
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Residues in contact with ARG1261 (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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1001A GLY 4.9 4.5 - - - +
1002A ILE* 3.3 25.9 + - - +
1003A ILE* 4.7 1.8 - - - +
1004A HIS* 3.2 28.5 + - - -
1134A LEU* 3.4 27.7 + - + +
1254A GLN* 5.0 6.9 + - - -
1257A MET* 3.0 34.6 + - - +
1258A THR* 3.5 26.3 + - - +
1260A MET* 1.3 78.7 - - - +
1262A GLN* 1.3 62.1 + - + +
1263A GLU 3.5 1.0 + - - -
1265A ARG* 3.2 24.7 + - - +
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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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1051A LYS* 2.7 33.0 + - + +
1258A THR* 3.1 40.9 + - - +
1259A TRP* 3.3 6.6 + - + +
1261A ARG* 1.3 80.2 - - - +
1263A GLU* 1.3 65.4 + - - +
1264A GLY 3.0 4.7 + - - -
1265A ARG* 3.1 51.5 + - - +
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Residues in contact with GLU1263 (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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1004A HIS* 3.7 15.1 + - - +
1005A ASN* 2.8 44.9 + - - +
1130A ARG* 4.4 1.6 - - - +
1177A ASN* 4.6 4.3 + - - -
1259A TRP* 3.5 57.3 + - + +
1260A MET 4.3 7.0 - - - +
1261A ARG 3.5 2.8 - - - -
1262A GLN* 1.3 72.0 - - - +
1264A GLY* 1.3 68.8 + - - +
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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
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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