Contacts of the helix formed by residues 1255 - 1262 (chain B) in PDB entry 1M7N
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 SER1255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1192B VAL* 4.3 3.8 - - - -
1253B ARG 3.8 1.0 + - - -
1254B PRO* 1.3 78.3 - - - +
1256B PHE* 1.3 65.3 + - - +
1257B LEU* 3.9 5.9 + - - +
1258B GLU* 3.1 31.4 + - - +
1259B ILE* 3.0 22.8 + - - +
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Residues in contact with PHE1256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117B ALA* 3.5 27.8 - - + +
1120B MET* 3.3 39.3 - - + -
1121B ALA* 3.7 9.9 - - + -
1124B ASN* 3.0 31.9 - - + -
1188B THR* 3.9 1.6 - - - -
1191B ASP* 3.5 20.2 - - + -
1192B VAL* 3.5 35.2 - - + -
1195B PHE* 3.8 24.0 - + + -
1255B SER* 1.3 74.7 - - - +
1257B LEU* 1.3 57.5 + - - +
1259B ILE* 3.0 11.4 + - + +
1260B ILE* 2.9 35.0 + - - +
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Residues in contact with LEU1257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121B ALA* 4.0 20.9 - - + +
1125B ALA* 6.3 1.3 - - + -
1255B SER* 3.3 7.0 + - - +
1256B PHE* 1.3 78.2 - - - +
1258B GLU* 1.3 57.5 + - - +
1260B ILE* 4.3 4.0 - - + -
1261B SER* 2.8 30.2 + - - -
1276B PHE* 4.4 9.9 - - + -
1277B TYR* 3.3 37.1 - - + -
1282B ASN* 3.2 37.0 - - - +
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Residues in contact with GLU1258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253B ARG 4.9 0.3 - - - +
1254B PRO* 3.5 26.7 - - + +
1255B SER* 3.1 25.1 + - - +
1256B PHE 3.1 0.4 - - - -
1257B LEU* 1.3 78.5 - - - +
1259B ILE* 1.3 64.5 + - - +
1261B SER* 3.4 7.9 + - - +
1262B SER* 3.2 24.6 + - - -
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Residues in contact with ILE1259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117B ALA* 4.4 6.1 - - + -
1192B VAL* 4.3 8.5 - - + -
1195B PHE* 3.6 46.4 - - + -
1241B LEU* 3.7 25.6 - - + -
1245B CYS* 3.9 15.0 - - - -
1254B PRO* 3.9 19.1 - - + -
1255B SER 3.0 19.0 + - - +
1256B PHE* 3.0 18.8 + - + +
1258B GLU* 1.3 73.6 - - - +
1260B ILE* 1.3 64.8 + - - +
1262B SER* 3.5 14.3 + - - -
1263B ILE* 3.2 20.0 - - + +
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Residues in contact with ILE1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B GLY* 4.3 6.1 - - - +
1117B ALA* 3.6 36.1 - - + +
1118B ASP* 3.6 25.4 - - + +
1121B ALA* 4.3 4.9 - - + -
1256B PHE 2.9 20.9 + - - +
1257B LEU* 3.8 5.6 - - + +
1259B ILE* 1.3 74.8 - - - +
1261B SER* 1.3 58.9 + - - +
1263B ILE* 2.9 29.7 + - + +
1264B LYS* 3.2 15.7 + - + +
1267B MET* 5.5 1.3 - - + -
1271B PHE* 3.8 22.2 - - + -
1277B TYR* 3.5 36.1 - - + -
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Residues in contact with SER1261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257B LEU 2.8 18.6 + - - -
1258B GLU* 3.5 12.5 - - - +
1260B ILE* 1.3 77.0 - - - +
1262B SER* 1.3 57.9 + - - +
1263B ILE 3.3 0.2 - - - -
1264B LYS* 2.7 29.6 + - - +
1277B TYR* 3.0 26.1 + - - -
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Residues in contact with SER1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237B MET* 6.0 0.3 - - - +
1241B LEU* 5.2 6.2 - - - +
1258B GLU 3.2 11.9 + - - -
1259B ILE* 3.5 11.6 + - - -
1260B ILE 3.2 0.4 - - - -
1261B SER* 1.3 77.0 - - - +
1263B ILE* 1.3 68.6 + - - +
1264B LYS 3.8 0.9 - - - -
1265B GLU* 6.1 1.3 - - - +
1266B GLU* 5.8 0.3 - - - +
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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