Contacts of the helix formed by residues 1296 - 1303 (chain B) in PDB entry 4DM8
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 ARG1296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1219B ARG* 3.6 23.3 - - - +
1279B TYR* 4.2 3.2 + - - -
1284B ASP* 2.8 53.0 + - - +
1295B ASN* 1.3 74.1 - - - +
1297B THR* 1.3 58.5 + - - +
1299B MET* 3.4 0.5 + - - +
1300B HIS* 3.0 27.4 + - - +
1308B THR* 3.5 13.4 - - + +
1309B ASP* 3.7 20.6 + - - +
1312B PHE* 3.3 45.6 - - + +
1313B THR* 5.5 1.0 + - - +
1316B ASN* 4.7 3.4 + - - -
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Residues in contact with THR1297 (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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1216B ALA 3.8 15.2 + - - +
1217B ASP 4.9 3.5 + - - -
1218B HIS* 3.1 45.3 - - - +
1219B ARG* 3.9 16.3 + - + +
1295B ASN* 3.1 9.4 + - - -
1296B ARG* 1.3 79.9 - - - +
1298B GLN* 1.3 55.3 + - - +
1300B HIS* 3.4 7.0 - - - +
1301B ASN* 2.7 40.5 + - - +
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Residues in contact with GLN1298 (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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1211B THR* 5.9 1.2 - - - -
1212B THR* 2.7 30.3 + - - +
1214B SER 3.1 16.5 - - - +
1215B SER 3.4 17.9 - - - +
1216B ALA* 3.1 13.9 - - - +
1226B LEU* 3.6 11.7 - - + +
1293B THR 4.2 3.0 + - - -
1294B LEU* 3.4 31.2 - - + +
1295B ASN* 2.7 43.9 + - - +
1297B THR* 1.3 71.0 - - - +
1299B MET* 1.3 59.7 + - - +
1301B ASN* 3.2 2.3 + - - +
1302B ALA* 2.8 31.9 + - - +
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Residues in contact with MET1299 (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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1275B ILE* 5.0 1.3 - - - -
1286B MET* 4.1 24.9 - - + +
1288B PHE* 3.2 28.5 - - + -
1294B LEU* 3.2 41.5 - - + +
1295B ASN 2.8 17.7 + - - +
1296B ARG 3.6 7.6 - - - +
1298B GLN* 1.3 77.0 - - - +
1300B HIS* 1.3 64.3 + - - +
1302B ALA* 3.3 12.1 + - + +
1304B PHE* 3.3 46.2 + - + -
1308B THR* 4.4 3.1 - - + -
1312B PHE* 3.9 27.8 - - + -
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Residues in contact with HIS1300 (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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1219B ARG* 3.4 46.4 + - + +
1220B VAL 3.0 25.4 - - - -
1221B ARG* 4.9 6.1 - - - +
1296B ARG 3.0 13.6 + - - +
1297B THR 3.4 8.5 - - - +
1299B MET* 1.3 77.7 - - - +
1301B ASN* 1.3 77.2 + - - +
1303B GLY* 3.3 6.6 + - - -
1305B GLY* 3.0 54.9 + - - +
1306B PRO* 5.4 0.4 - - - +
1308B THR* 3.2 17.9 + - + +
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Residues in contact with ASN1301 (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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1215B SER* 3.1 36.6 + - - +
1218B HIS 3.2 16.6 + - - -
1219B ARG* 3.4 1.0 - - - -
1220B VAL* 2.8 43.8 + - + +
1222B LEU* 3.6 7.6 - - - +
1223B ASP* 2.9 30.8 + - + +
1226B LEU* 4.2 2.0 - - + -
1297B THR* 2.7 21.2 + - - +
1298B GLN 3.2 2.9 + - - +
1300B HIS* 1.3 89.8 + - - +
1302B ALA* 1.3 63.3 + - - +
1303B GLY* 3.1 3.0 + - - -
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Residues in contact with ALA1302 (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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1222B LEU* 4.0 1.1 - - - -
1226B LEU* 3.8 18.1 - - + +
1227B TRP* 3.4 31.6 - - - +
1230B PHE* 3.6 30.8 - - + -
1294B LEU* 4.6 9.2 - - + -
1298B GLN 2.8 17.1 + - - +
1299B MET* 3.3 13.2 + - + +
1301B ASN* 1.3 76.6 - - - +
1303B GLY* 1.3 57.5 + - - +
1304B PHE* 3.9 0.7 - - + -
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Residues in contact with GLY1303 (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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1222B LEU* 3.8 17.0 - - - -
1227B TRP* 4.8 0.9 - - - -
1230B PHE* 5.1 2.2 - - - -
1300B HIS 3.3 2.2 + - - -
1301B ASN 3.1 4.2 - - - -
1302B ALA* 1.3 80.7 - - - +
1304B PHE* 1.3 60.4 + - - +
1305B GLY 3.1 2.9 - - - -
1396B ARG* 2.8 30.5 + - - +
1400B LEU* 3.7 18.7 - - - +
1501B REA 4.3 4.0 - - - -
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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