Contacts of the helix formed by residues 1256 - 1264 (chain B) in PDB entry 1CM8
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 ASP1256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1253B LEU 5.1 0.7 - - - +
1254B GLN 3.3 10.7 + - - +
1255B SER* 1.3 67.7 + - - +
1257B GLU* 1.3 67.7 + - - +
1259B LYS* 3.0 22.2 + - - +
1260B ASN* 2.8 38.0 + - - +
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Residues in contact with GLU1257 (chain B).
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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1197B ILE* 4.7 4.9 - - - +
1231B HIS* 3.0 36.5 + - - -
1232B LEU* 3.7 21.8 - - + +
1255B SER* 4.1 7.0 + - - +
1256B ASP* 1.3 77.8 - - - +
1258B ALA* 1.3 63.7 + - - +
1260B ASN* 3.6 6.7 + - - +
1261B TYR* 3.1 23.2 + - - +
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Residues in contact with ALA1258 (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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1197B ILE* 3.9 21.5 - - + +
1198B LEU* 4.0 21.8 - - + +
1232B LEU* 4.9 6.1 - - - -
1235B LEU* 5.4 0.4 - - - -
1253B LEU* 4.3 5.8 - - + -
1255B SER* 3.4 24.1 + - - +
1256B ASP 3.2 0.8 - - - -
1257B GLU* 1.3 79.5 + - - +
1259B LYS* 1.3 58.8 + - - +
1261B TYR* 3.5 4.8 + - - +
1262B MET* 3.0 34.7 + - - +
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Residues in contact with LYS1259 (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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1250B VAL* 3.1 21.0 - - - +
1251B GLN 3.5 20.4 - - - +
1253B LEU* 3.9 25.2 + - + +
1255B SER 2.9 18.2 + - - +
1256B ASP* 3.0 21.2 + - - +
1258B ALA* 1.3 74.5 - - - +
1260B ASN* 1.3 84.8 + - - +
1262B MET* 3.5 1.0 + - - -
1263B LYS* 3.0 44.5 + - + +
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Residues in contact with ASN1260 (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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1256B ASP* 2.8 27.5 + - - +
1257B GLU* 4.0 5.2 - - - +
1259B LYS* 1.3 92.9 - - - +
1261B TYR* 1.3 64.7 + - - +
1263B LYS* 3.1 19.5 + - - +
1264B GLY* 3.1 11.8 + - - -
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Residues in contact with TYR1261 (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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1232B LEU* 3.0 60.3 + - + -
1233B ASP* 3.6 7.1 + - + -
1235B LEU* 4.0 23.8 - - + -
1236B LYS* 3.0 34.9 - - - +
1257B GLU 3.1 18.1 + - - +
1258B ALA* 3.8 3.4 - - - +
1260B ASN* 1.3 78.5 - - - +
1262B MET* 1.3 67.5 + - - +
1263B LYS 3.1 1.2 + - - -
1264B GLY* 3.3 1.9 + - - -
1265B LEU* 3.1 43.4 + - + +
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Residues in contact with MET1262 (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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1198B LEU* 3.8 21.1 - - + -
1235B LEU* 4.5 7.9 - - + -
1239B MET* 3.5 29.4 - - + -
1244B THR* 4.6 4.0 - - + -
1245B PRO* 3.3 37.5 - - + -
1250B VAL* 3.6 29.5 - - + +
1253B LEU* 4.4 4.7 - - + -
1258B ALA 3.0 21.3 + - - +
1261B TYR* 1.3 79.8 - - + +
1263B LYS* 1.3 62.4 + - - +
1265B LEU* 3.5 34.8 - - + +
1266B PRO 5.1 0.7 - - - +
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Residues in contact with LYS1263 (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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1247B ALA 6.0 0.2 - - - +
1250B VAL* 4.0 15.5 - - + +
1251B GLN* 3.6 35.4 + - + +
1259B LYS* 3.0 38.0 + - + +
1260B ASN* 3.1 16.9 - - - +
1261B TYR 3.1 0.2 - - - -
1262B MET* 1.3 75.3 - - - +
1264B GLY* 1.3 66.0 + - - +
1265B LEU 3.2 9.0 + - - +
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Residues in contact with GLY1264 (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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1260B ASN 3.1 9.3 + - - -
1261B TYR 3.9 2.5 - - - -
1263B LYS* 1.3 77.5 - - - +
1265B LEU* 1.3 63.5 + - - +
1266B PRO* 3.6 4.9 - - - +
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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