Contacts of the helix formed by residues 1395 - 1401 (chain A) in PDB entry 4V1M
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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859A SER* 5.0 1.6 + - - -
1393A ASN 4.7 0.4 - - - -
1394A THR* 1.3 75.1 - - - +
1396A ALA* 1.4 56.1 + - - -
1398A MET* 2.9 27.4 + - - +
1399A ARG* 2.9 11.1 + - - -
1417A GLU* 5.4 0.7 - - - -
1418A LEU 5.8 0.9 - - - -
1419A ASP* 3.3 28.9 - - - -
1420A ASP* 5.7 1.3 - - - -
1426A GLU* 4.0 7.8 + - - -
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Residues in contact with ALA1396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.3 16.4 - - + -
1395A GLY* 1.4 68.0 - - - -
1397A LEU* 1.3 53.9 + - - +
1399A ARG* 3.2 19.4 + - - +
1400A CYS* 2.8 38.7 + - - +
1408A ILE* 3.7 6.5 - - + +
1409A LEU* 4.8 3.4 - - + -
1412A ALA* 3.8 24.0 - - + -
1417A GLU* 3.4 19.8 + - + +
1419A ASP* 3.4 3.9 + - + +
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Residues in contact with LEU1397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.7 31.6 - - + -
19A PHE* 4.0 16.8 - - + -
1395A GLY 3.1 0.2 + - - -
1396A ALA* 1.3 75.6 - - - +
1398A MET* 1.3 64.0 + - - +
1400A CYS* 3.1 25.2 - - - -
1401A SER* 3.3 4.0 + - - -
1409A LEU* 4.4 15.9 - - + -
1419A ASP* 3.3 12.0 + - - +
1426A GLU* 3.3 19.3 - - + +
1429A ILE* 3.9 43.7 - - + +
1430A LEU* 5.3 4.7 - - + -
1203B LEU* 4.5 13.7 - - + -
1204B PHE* 4.8 11.9 - - + -
1207B LEU* 5.8 0.9 - - + -
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Residues in contact with MET1398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A LYS* 5.2 1.4 - - - +
846A GLU* 3.4 36.7 - - + +
847A ASP* 3.7 22.2 - - + +
859A SER* 3.8 21.5 - - - -
1390A ASN* 5.0 0.2 - - - +
1394A THR* 3.9 17.9 - - - +
1395A GLY 2.9 11.3 + - - +
1397A LEU* 1.3 69.9 - - - +
1399A ARG* 1.4 64.9 + - + +
1401A SER* 2.6 26.0 + - - -
1402A PHE* 4.4 1.2 + - - +
1423A GLY* 4.0 13.2 - - - -
1424A VAL 4.1 3.1 - - - +
1425A SER* 3.5 24.2 - - - +
1426A GLU* 2.8 24.6 + - - +
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Residues in contact with ARG1399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 5.6 4.6 - - - +
1390A ASN* 2.9 52.3 + - - +
1391A ARG* 5.5 2.0 - - - +
1392A SER 3.3 22.7 + - - -
1394A THR* 2.6 39.7 + - - +
1395A GLY 2.9 7.2 + - - +
1396A ALA* 3.2 21.5 - - - +
1398A MET* 1.4 77.2 - - + +
1400A CYS* 1.3 60.6 + - - +
1401A SER 3.1 1.6 + - - -
1402A PHE 3.1 13.7 + - - +
1408A ILE* 3.5 28.0 - - + +
1417A GLU* 2.7 36.6 + - - -
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Residues in contact with CYS1400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ILE* 3.8 31.2 - - - +
1396A ALA 2.8 19.0 + - - +
1397A LEU* 3.1 25.8 + - - -
1399A ARG* 1.3 72.0 - - - +
1401A SER* 1.3 57.6 + - - +
1402A PHE 3.2 3.2 + - - -
1405A THR* 2.9 55.4 + - - +
1408A ILE* 3.9 8.4 - - + +
1409A LEU* 4.0 18.6 - - + -
1429A ILE* 5.2 0.4 - - - -
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Residues in contact with SER1401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ILE* 3.6 13.7 - - - -
337A ARG* 3.5 14.2 - - - +
341A MET* 4.1 29.2 - - - -
839A ARG* 2.8 25.0 + - - -
843A LYS* 3.3 23.0 + - - +
1397A LEU 3.3 9.1 + - - -
1398A MET* 2.6 21.8 + - - -
1399A ARG 3.1 0.8 - - - -
1400A CYS* 1.3 75.1 - - - +
1402A PHE* 1.4 50.5 + - - +
1405A THR* 5.1 0.7 - - - -
1425A SER* 4.1 4.8 + - - -
1429A ILE* 5.0 0.7 - - - -
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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