Contacts of the helix formed by residues 1247 - 1259 (chain A) in PDB entry 5M64
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 SER1247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1245A ASP 3.7 3.3 + - - -
1246A VAL* 1.3 78.2 - - - +
1248A ASP* 1.3 62.3 + - - +
1249A GLU* 2.6 37.9 + - - -
1250A GLN* 3.1 9.2 + - - +
1251A ALA* 3.0 25.3 + - - +
1517A ARG* 3.4 10.8 - - - +
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Residues in contact with ASP1248 (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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1247A SER* 1.3 75.1 - - - +
1249A GLU* 1.3 60.8 + - - +
1250A GLN 3.1 1.5 + - - -
1251A ALA* 3.3 13.9 + - - +
1252A ASP* 3.4 15.2 + - - +
1509A HIS* 2.9 34.9 + - + -
1512A PRO* 6.2 0.2 - - - +
1517A ARG* 2.5 33.1 + - - +
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Residues in contact with GLU1249 (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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1247A SER* 2.6 27.2 + - - +
1248A ASP* 1.3 77.6 - - - +
1250A GLN* 1.3 86.6 + - - +
1252A ASP* 2.8 18.0 - - - +
1253A THR* 3.9 7.6 - - - +
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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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1246A VAL* 4.0 14.6 - - + -
1247A SER* 3.1 13.9 + - - +
1249A GLU* 1.3 110.3 + - - +
1251A ALA* 1.3 59.4 + - - +
1252A ASP 3.4 1.6 - - - -
1253A THR* 2.3 41.3 + - - +
1254A PHE* 3.2 15.6 - - + -
1535A PHE* 5.6 3.7 - - + -
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Residues in contact with ALA1251 (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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1242A ILE* 5.8 8.3 - - + -
1246A VAL* 4.7 6.3 - - + +
1247A SER 3.0 15.1 + - - +
1248A ASP* 3.3 6.2 + - - +
1250A GLN* 1.3 76.5 - - - +
1252A ASP* 1.3 60.0 + - - +
1254A PHE* 3.1 13.0 + - - +
1255A CYS* 2.9 31.2 + - - -
1509A HIS* 3.8 28.0 - - + +
1517A ARG* 5.6 1.1 - - - +
1519A LEU* 5.2 8.2 - - + +
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Residues in contact with ASP1252 (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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1248A ASP 3.5 9.4 + - - +
1249A GLU* 2.8 30.1 - - - +
1251A ALA* 1.3 73.9 - - - +
1253A THR* 1.3 64.2 + - - +
1255A CYS* 3.3 14.2 - - + +
1256A LYS* 2.9 44.7 + - - +
1509A HIS* 5.6 3.5 - - + +
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Residues in contact with THR1253 (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 GLU 3.9 10.1 - - - +
1250A GLN* 2.3 40.3 + - - +
1252A ASP* 1.3 94.4 + - - +
1254A PHE* 1.3 65.7 + - - +
1256A LYS* 3.5 7.5 + - - +
1257A SER* 2.9 32.7 + - - -
1307A ASP* 4.9 0.3 - - - +
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Residues in contact with PHE1254 (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 VAL* 5.6 1.1 - - + -
1250A GLN* 3.2 31.9 - - + -
1251A ALA* 3.1 9.7 + - - +
1253A THR* 1.3 84.6 + - - +
1255A CYS* 1.3 60.8 + - - +
1257A SER* 4.2 8.1 - - - -
1258A ILE* 2.9 50.1 + - + +
1507A CYS* 5.8 0.4 - - - -
1519A LEU* 5.6 8.3 - - + -
1532A GLN* 5.3 14.6 - - + -
1535A PHE* 3.4 59.2 - + + -
1536A ILE* 6.3 2.2 - - + -
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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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1251A ALA 2.9 25.4 + - - -
1252A ASP* 3.2 17.5 + - + +
1254A PHE* 1.3 77.0 - - - +
1256A LYS* 1.3 57.9 + - + +
1259A SER* 2.9 35.2 + - - -
1507A CYS* 4.2 23.0 - - - +
1508A VAL* 4.5 0.9 - - - -
1509A HIS* 4.0 19.1 - - - -
1519A LEU* 3.7 29.8 - - - -
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Residues in contact with LYS1256 (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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1252A ASP* 2.9 31.0 + - + +
1253A THR* 3.9 6.3 - - - +
1255A CYS* 1.3 77.7 - - + +
1257A SER* 1.3 52.0 + - - +
1259A SER* 3.5 11.4 - - - +
1261A VAL* 5.2 2.3 - - - +
1304A GLU* 4.4 12.1 - - - +
1305A GLU* 3.0 47.1 + - - +
1306A TYR* 5.5 2.8 - - + -
1307A ASP* 3.3 23.3 - - + +
1499A ARG* 2.5 28.3 + - - -
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Residues in contact with SER1257 (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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1253A THR* 2.9 21.6 + - - -
1254A PHE* 4.0 11.1 - - - -
1256A LYS* 1.3 77.8 - - - +
1258A ILE* 1.3 62.6 + - - +
1307A ASP* 3.3 14.7 + - - -
1499A ARG* 3.1 32.1 + - - +
1501A ILE* 5.9 0.2 - - - +
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Residues in contact with ILE1258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1238A MET* 6.2 1.1 - - + -
1240A LEU* 5.6 9.9 - - + -
1254A PHE* 2.9 35.1 + - + +
1255A CYS 4.5 0.7 - - - +
1257A SER* 1.3 79.4 - - - +
1259A SER* 1.3 65.7 + - - +
1260A LYS 3.1 4.5 + - - -
1499A ARG* 6.0 0.7 - - - +
1501A ILE* 3.6 35.4 - - + +
1504A ILE* 4.4 21.7 - - + +
1507A CYS* 5.0 14.6 - - + -
1519A LEU* 5.9 5.4 - - + -
1521A THR* 5.1 4.7 - - + -
1529A MET* 6.2 3.8 - - + -
1532A GLN* 6.3 2.5 - - + -
1536A ILE* 6.4 2.5 - - + -
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Residues in contact with SER1259 (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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1255A CYS 2.9 20.9 + - - -
1256A LYS* 3.5 16.2 - - - +
1258A ILE* 1.3 75.2 - - - +
1260A LYS* 1.3 65.1 + - - +
1261A VAL* 3.5 10.7 + - - +
1499A ARG* 3.6 8.2 + - - -
1505A ASP 3.4 12.5 + - - -
1506A ARG* 3.5 19.6 - - - +
1507A CYS* 3.9 15.6 - - - +
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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