Contacts of the helix formed by residues 1362 - 1372 (chain A) in PDB entry 3MB3
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 ASP1362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1341A PHE* 3.7 8.3 - - - +
1343A GLN* 3.3 22.1 - - - +
1344A PRO* 3.1 34.9 - - + +
1360A PRO* 6.1 0.2 - - - +
1361A MET* 1.3 81.2 - - - +
1363A PHE* 1.3 61.3 + - - +
1364A ALA* 3.0 9.2 + - - +
1365A THR* 2.5 38.0 + - - +
1366A VAL* 3.1 19.8 + - - +
1388A ILE* 3.5 10.8 - - - -
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Residues in contact with PHE1363 (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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1329A LEU* 3.7 27.2 - - + +
1332A ILE* 3.8 36.1 - - + -
1333A PHE* 3.4 28.2 - + + -
1338A SER* 4.9 4.9 - - - -
1341A PHE* 3.0 43.3 + - + +
1342A ARG* 4.4 1.8 - - + -
1362A ASP* 1.3 69.2 - - - +
1364A ALA* 1.3 65.0 + - - +
1366A VAL* 3.4 5.4 + - + +
1367A ARG* 3.0 19.1 + - - +
1385A VAL* 3.9 18.6 - - + -
1388A ILE* 3.8 25.1 - - + -
1389A PHE* 3.8 22.9 - + - -
1410A LEU* 4.0 10.1 - - + -
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Residues in contact with ALA1364 (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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1333A PHE* 3.6 12.1 - - + -
1342A ARG 3.1 22.2 + - - +
1343A GLN* 3.6 21.1 - - - +
1344A PRO* 4.8 2.2 - - + -
1362A ASP* 3.0 8.0 + - - +
1363A PHE* 1.3 77.0 - - - +
1365A THR* 1.3 57.7 + - - +
1367A ARG* 3.3 5.1 + - - +
1368A GLU* 2.9 40.6 + - - +
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Residues in contact with THR1365 (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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1344A PRO* 4.2 8.5 - - - +
1361A MET* 3.9 23.1 - - + -
1362A ASP* 2.5 35.2 + - - +
1364A ALA* 1.3 74.7 - - - +
1366A VAL* 1.3 62.3 + - - +
1368A GLU* 3.3 13.1 + - + +
1369A THR* 2.8 36.2 + - - +
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Residues in contact with VAL1366 (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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1329A LEU* 3.9 16.4 - - + -
1361A MET* 3.8 21.5 - - + -
1362A ASP 3.1 14.0 + - - +
1363A PHE* 3.9 8.1 - - - +
1364A ALA 3.3 0.2 - - - -
1365A THR* 1.3 74.8 - - - +
1367A ARG* 1.3 63.8 + - - +
1369A THR* 3.3 1.3 + - - -
1370A LEU* 3.1 20.3 + - - +
1375A TYR* 3.5 24.1 - - - +
1381A LEU* 3.9 23.6 - - + +
1384A ASP* 3.9 9.9 - - + -
1385A VAL* 4.0 15.0 - - + +
1388A ILE* 4.3 11.0 - - + -
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Residues in contact with ARG1367 (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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1326A GLU* 3.8 12.1 - - - +
1329A LEU* 4.1 17.9 - - + +
1330A ASN* 3.1 31.3 + - - +
1333A PHE* 3.2 57.6 - - + +
1363A PHE 3.0 17.0 + - - +
1364A ALA* 3.7 5.6 + - - +
1365A THR 3.2 0.2 - - - -
1366A VAL* 1.3 75.9 - - - +
1368A GLU* 1.3 65.5 + - - +
1369A THR 3.3 0.2 + - - -
1370A LEU* 3.3 2.9 + - - +
1371A GLU* 2.9 45.4 + - - +
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Residues in contact with GLU1368 (chain A).
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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1364A ALA* 2.9 29.3 + - + +
1365A THR* 3.3 11.5 + - + +
1367A ARG* 1.3 76.0 - - - +
1369A THR* 1.3 57.3 + - - +
1371A GLU* 3.4 9.9 + - - +
1372A ALA* 2.9 32.5 + - - +
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Residues in contact with THR1369 (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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1365A THR* 2.8 25.7 + - - +
1366A VAL 3.6 4.5 - - - -
1367A ARG 3.2 0.2 - - - -
1368A GLU* 1.3 75.7 - - - +
1370A LEU* 1.3 61.1 + - - +
1372A ALA* 3.4 4.5 + - - +
1373A GLY 3.3 3.6 + - - -
1374A ASN* 2.9 51.7 + - + +
1375A TYR* 3.5 33.4 + - + +
1384A ASP* 4.9 2.7 + - - +
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Residues in contact with LEU1370 (chain A).
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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1321A TRP* 4.0 28.5 - - + -
1322A LYS* 3.9 19.1 - - + +
1325A CYS* 3.9 8.5 - - + -
1326A GLU* 3.7 44.4 - - + +
1329A LEU* 4.0 13.9 - - + -
1366A VAL 3.1 13.1 + - - +
1367A ARG* 3.6 8.1 - - - +
1369A THR* 1.3 73.6 - - - +
1371A GLU* 1.3 67.8 + - - +
1373A GLY* 3.1 14.1 + - - +
1374A ASN 4.9 0.7 - - - +
1375A TYR* 3.6 14.2 - - + -
1381A LEU* 4.1 9.9 - - + -
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Residues in contact with GLU1371 (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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1326A GLU* 3.6 25.1 - - - +
1367A ARG* 2.9 47.5 + - - +
1368A GLU* 3.8 8.0 - - - +
1370A LEU* 1.3 74.2 - - - +
1372A ALA* 1.3 60.2 - - - +
1373A GLY* 3.2 1.6 + - - -
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Residues in contact with ALA1372 (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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1368A GLU 2.9 18.3 + - - +
1369A THR* 3.7 7.0 - - - +
1370A LEU 3.3 0.2 - - - -
1371A GLU* 1.3 74.7 - - - +
1373A GLY* 1.3 59.1 + - - +
1374A ASN* 3.4 23.9 + - - +
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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