Contacts of the helix formed by residues 1261 - 1269 (chain M) in PDB entry 3HOU
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 LYS1261 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1152M ILE* 3.4 20.4 - - + -
1257M ASP* 3.1 31.9 + - - +
1258M HIS* 3.9 17.1 + - - +
1259M MET 2.9 0.6 - - - -
1260M LEU* 1.3 77.6 - - - +
1262M LYS* 1.3 61.3 + - + +
1263M ILE 3.1 1.6 - - - -
1264M GLU* 3.1 29.9 + - + +
1265M ASN* 3.3 6.8 + - - +
265N SER* 5.4 0.7 + - - -
312N GLU* 6.1 0.7 - - - -
16U PRO* 6.1 1.0 - - - +
43U VAL* 4.6 5.3 + - - +
44U TYR* 3.6 41.8 - - + +
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Residues in contact with LYS1262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255M GLU* 4.9 9.3 + - - -
1258M HIS* 2.9 31.5 + - - +
1259M MET* 3.3 45.6 - - + +
1261M LYS* 1.3 76.9 - - + +
1263M ILE* 1.3 59.7 + - - +
1265M ASN* 3.6 6.9 + - - +
1266M THR* 3.1 26.2 + - - -
265N SER* 5.2 8.3 - - - +
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Residues in contact with ILE1263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193M LEU* 4.6 9.2 - - + -
1220M PHE* 3.7 32.5 - - + -
1223M ASP 6.1 0.2 - - - +
1224M LEU* 4.9 9.4 - - + -
1240M CYS* 6.5 0.2 - - + -
1242M VAL* 4.2 23.3 - - + -
1259M MET* 3.1 44.8 + - + +
1260M LEU* 3.8 10.3 - - + +
1262M LYS* 1.3 76.0 - - - +
1264M GLU* 1.3 60.5 + - - +
1265M ASN 3.2 2.0 - - - -
1266M THR* 4.0 6.6 - - - -
1267M MET* 3.0 30.0 + - + +
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Residues in contact with GLU1264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150M SER* 2.7 30.0 + - - -
1152M ILE* 5.7 2.2 - - + -
1193M LEU* 4.0 17.4 - - + +
1195M LEU* 5.2 0.7 - - - +
1260M LEU 3.2 15.0 + - - +
1261M LYS* 3.1 22.4 + - + +
1263M ILE* 1.3 79.5 - - - +
1265M ASN* 1.3 71.2 + - - +
1267M MET* 3.6 7.5 - - - +
1268M LEU* 3.4 24.9 + - - +
44U TYR* 3.9 17.8 + - + -
46U HIS* 2.9 30.5 + - - -
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Residues in contact with ASN1265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261M LYS 3.3 6.9 + - - +
1262M LYS 3.8 7.4 - - - +
1264M GLU* 1.3 91.7 - - - +
1266M THR* 1.3 57.1 + - - +
1267M MET 2.6 15.9 + - - -
1268M LEU* 2.6 18.3 + - - +
1269M GLU* 2.8 22.4 + - - +
263N GLY* 3.5 22.6 + - - +
264N SER* 3.9 3.4 - - - +
265N SER* 2.9 42.3 + - - +
46U HIS* 5.4 1.7 + - - -
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Residues in contact with THR1266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219M THR* 5.3 9.0 - - + -
1220M PHE* 4.3 20.4 - - + -
1262M LYS 3.1 17.1 + - - -
1263M ILE* 4.0 9.1 - - - -
1265M ASN* 1.3 78.7 - - - +
1267M MET* 1.3 57.7 + - - +
1270M ASN* 3.0 53.6 + - + +
1271M ILE* 3.8 2.1 + - - +
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Residues in contact with MET1267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143M LEU* 3.4 29.4 - - + +
1193M LEU* 4.0 25.1 - - + -
1195M LEU* 3.2 45.3 - - + -
1216M ILE* 3.8 26.5 - - - -
1220M PHE* 3.7 21.1 - - + -
1224M LEU* 5.3 0.4 - - - -
1240M CYS* 4.7 9.2 - - - -
1263M ILE* 3.0 22.8 + - + +
1264M GLU* 3.6 7.9 - - - +
1265M ASN 2.6 4.8 + - - -
1266M THR* 1.3 74.4 - - - +
1268M LEU* 1.3 64.1 + - + +
1271M ILE* 3.5 19.5 + - + +
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Residues in contact with LEU1268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142M THR* 4.7 4.2 + - - -
1143M LEU* 4.6 3.6 - - + -
1144M LYS* 2.9 44.6 + - + +
1147M THR* 3.5 30.5 - - + +
1150M SER* 4.7 4.0 - - - +
1195M LEU* 5.7 5.2 - - + -
1264M GLU* 3.4 35.6 + - - +
1265M ASN* 2.6 14.0 + - - +
1267M MET* 1.3 79.1 - - + +
1269M GLU* 1.3 67.2 + - + +
1271M ILE 5.3 0.2 - - - -
46U HIS* 4.0 16.4 - - + +
48U LEU* 3.5 32.1 - - + -
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Residues in contact with GLU1269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142M THR* 5.8 5.2 - - - -
1144M LYS* 3.0 33.7 + - + +
1265M ASN* 2.8 16.5 + - - +
1266M THR 4.0 0.2 - - - -
1268M LEU* 1.3 93.1 - - + +
1270M ASN* 1.3 71.9 + - - +
1271M ILE 4.6 0.4 - - - +
262N GLU 3.8 11.5 - - - +
263N GLY* 3.4 24.7 - - - -
264N SER 4.4 3.1 + - - -
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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