Contacts of the helix formed by residues 1395 - 1400 (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 GLY1395 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1393M ASN 3.6 1.1 + - - -
1394M THR* 1.3 81.2 - - - +
1396M ALA* 1.3 69.3 + - - +
1397M LEU 3.3 0.2 - - - -
1398M MET* 2.9 12.2 + - - +
1399M ARG* 3.0 10.4 + - - -
1418M LEU 5.4 2.2 - - - -
1419M ASP* 2.9 29.6 - - - -
1420M ASP 5.6 0.4 - - - -
1426M GLU* 3.9 7.6 + - - -
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Residues in contact with ALA1396 (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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19M PHE* 3.8 24.2 - - + -
1395M GLY* 1.3 68.9 - - - -
1397M LEU* 1.3 55.3 + - - +
1399M ARG* 2.9 28.7 + - - +
1400M CYS* 2.7 37.2 + - - +
1408M ILE* 4.0 5.8 - - + +
1409M LEU* 4.5 4.3 - - + -
1412M ALA* 3.8 22.7 - - + -
1417M GLU* 3.9 8.0 + - + +
1418M LEU 6.1 0.4 - - - -
1419M ASP* 3.2 3.8 + - + +
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Residues in contact with LEU1397 (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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17M VAL* 3.9 31.0 - - + -
19M PHE* 3.9 21.8 - - + -
1395M GLY 3.3 0.4 - - - -
1396M ALA* 1.3 78.2 - - - +
1398M MET* 1.3 62.5 + - - +
1400M CYS* 3.0 27.5 - - - -
1401M SER* 3.6 3.1 + - - -
1409M LEU* 4.6 5.1 - - + +
1419M ASP* 3.4 5.1 + - - +
1421M CYS* 5.3 0.4 - - - -
1425M SER* 5.4 0.2 - - - -
1426M GLU* 3.1 27.8 - - + +
1429M ILE* 3.9 44.4 - - + +
1430M LEU* 5.3 5.2 - - + -
1203N LEU* 4.5 14.8 - - + -
1204N PHE* 5.0 9.2 - - + -
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Residues in contact with MET1398 (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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846M GLU* 2.8 40.8 - - + +
847M ASP* 4.4 8.7 - - + +
859M SER* 4.0 7.4 - - - -
1394M THR* 2.9 36.1 - - + -
1395M GLY 2.9 7.9 + - - +
1397M LEU* 1.3 77.8 - - - +
1399M ARG* 1.3 64.8 + - + +
1401M SER* 2.6 28.4 + - - -
1402M PHE* 5.2 0.9 - - - +
1423M GLY* 4.1 3.1 - - - -
1424M VAL 4.0 11.0 - - - +
1425M SER* 3.6 31.2 - - - +
1426M GLU* 3.2 23.0 + - - +
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Residues in contact with ARG1399 (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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132M LYS* 5.8 3.6 - - - +
1390M ASN* 3.0 54.6 + - - +
1391M ARG* 4.5 1.8 - - - +
1392M SER 3.9 18.6 + - - +
1393M ASN* 5.6 0.2 - - - +
1394M THR* 3.0 34.6 + - - +
1395M GLY 3.0 1.8 + - - +
1396M ALA* 2.9 39.1 + - - +
1398M MET* 1.3 81.9 - - + +
1400M CYS* 1.3 58.7 + - - +
1401M SER 2.9 5.9 + - - -
1402M PHE* 3.1 20.4 + - - +
1408M ILE* 3.5 29.5 - - + +
1417M GLU* 3.0 22.6 + - - -
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Residues in contact with CYS1400 (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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336M ILE* 3.9 26.3 - - - +
1396M ALA 2.7 11.7 + - - +
1397M LEU* 3.0 26.9 - - - -
1398M MET 3.2 1.0 - - - -
1399M ARG* 1.3 73.0 - - - +
1401M SER* 1.3 56.6 + - - +
1402M PHE 3.1 5.2 + - - -
1405M THR* 3.1 41.5 + - - +
1408M ILE* 3.9 11.4 - - + +
1409M LEU* 3.3 38.1 - - + -
1429M ILE* 4.9 0.4 - - - -
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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