Contacts of the helix formed by residues 1320 - 1335 (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 ALA1320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1316A TYR* 6.1 0.9 - - + -
1317A ASP* 3.2 40.8 + - + +
1319A GLN* 1.3 75.8 - - - +
1321A TRP* 1.3 57.4 + - - +
1322A LYS 3.1 5.5 + - - -
1323A LYS* 3.4 7.7 + - - +
1324A GLN* 3.4 36.4 + - - +
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Residues in contact with TRP1321 (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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1317A ASP 4.9 0.4 + - - -
1318A ILE 3.1 27.8 + - - -
1319A GLN* 2.8 9.4 + - - +
1320A ALA* 1.3 71.9 - - - +
1322A LYS* 1.3 90.9 + - + +
1324A GLN* 3.6 15.7 + - - +
1325A CYS* 3.0 43.7 + - - -
1370A LEU* 4.0 22.4 - - + -
1375A TYR* 3.4 31.6 - - + -
1376A GLU 4.2 4.7 + - - -
1377A SER* 3.8 17.9 - - - +
1378A PRO* 3.6 38.3 - - + +
1381A LEU* 5.1 2.5 - - + -
1421A VAL* 3.8 20.4 - - + +
1425A TYR* 3.9 19.2 - + + -
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Residues in contact with LYS1322 (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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1319A GLN* 2.7 50.8 + - + +
1321A TRP* 1.3 118.0 - - + +
1323A LYS* 1.3 60.4 + - - +
1325A CYS* 3.3 4.2 + - - +
1326A GLU* 2.9 27.5 + - - +
1370A LEU* 3.9 14.6 - - + +
1373A GLY* 6.2 3.8 - - - -
1375A TYR 4.9 4.5 - - - -
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Residues in contact with LYS1323 (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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1319A GLN 4.6 0.2 + - - -
1320A ALA* 3.4 8.0 + - - +
1322A LYS* 1.3 74.5 - - - +
1324A GLN* 1.3 67.3 + - + +
1326A GLU* 2.9 18.9 + - + +
1327A GLU* 2.8 51.5 + - + +
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Residues in contact with GLN1324 (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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1320A ALA* 3.4 29.6 + - - +
1321A TRP* 3.6 11.7 + - - +
1322A LYS 3.3 0.4 - - - -
1323A LYS* 1.3 76.9 - - + +
1325A CYS* 1.3 57.7 + - - +
1327A GLU* 3.6 12.8 + - - +
1328A LEU* 3.0 27.9 + - - +
1421A VAL* 3.4 44.9 - - + +
1424A ASP* 4.5 17.4 + - - +
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Residues in contact with CYS1325 (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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1321A TRP* 3.0 37.9 + - - +
1322A LYS 3.7 3.8 - - - +
1324A GLN* 1.3 74.5 - - - +
1326A GLU* 1.3 66.7 + - - +
1328A LEU* 4.0 6.5 - - - +
1329A LEU* 3.0 28.8 + - + +
1370A LEU* 3.9 15.0 - - + -
1378A PRO* 4.6 4.3 - - - -
1381A LEU* 4.0 23.3 - - + -
1418A ILE* 4.0 25.6 - - - -
1421A VAL* 4.1 8.7 - - - -
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Residues in contact with GLU1326 (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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1322A LYS 2.9 15.6 + - - +
1323A LYS* 3.3 24.0 - - + +
1325A CYS* 1.3 77.2 - - - +
1327A GLU* 1.3 58.2 + - + +
1329A LEU* 3.7 3.0 - - - +
1330A ASN* 2.9 45.3 + - - +
1367A ARG* 3.8 17.7 - - - +
1370A LEU* 3.7 15.1 - - + +
1371A GLU* 3.6 36.2 - - - +
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Residues in contact with GLU1327 (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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1323A LYS* 2.8 40.0 + - + +
1324A GLN* 3.8 10.9 - - - +
1326A GLU* 1.3 74.6 - - + +
1328A LEU* 1.3 65.3 + - - +
1330A ASN* 3.2 11.3 + - - +
1331A LEU* 3.0 29.7 + - + +
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Residues in contact with LEU1328 (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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1324A GLN 3.0 18.9 + - - +
1325A CYS* 3.3 6.2 + - - +
1327A GLU* 1.3 74.4 - - - +
1329A LEU* 1.3 58.6 + - + +
1331A LEU* 3.2 12.0 + - + +
1332A ILE* 3.0 39.4 + - + +
1413A PHE* 3.9 26.2 - - + +
1414A PHE* 4.0 26.5 - - + +
1417A HIS* 3.7 37.0 - - + +
1418A ILE* 4.2 19.5 - - + +
1421A VAL* 5.2 3.1 - - + -
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Residues in contact with LEU1329 (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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1325A CYS* 3.0 21.7 + - + +
1326A GLU* 3.7 4.0 - - - +
1328A LEU* 1.3 75.3 - - + +
1330A ASN* 1.3 63.5 + - - +
1332A ILE* 3.2 10.0 + - + +
1333A PHE* 2.9 36.2 + - + +
1363A PHE* 3.7 35.2 - - + +
1366A VAL* 3.9 27.6 - - + -
1367A ARG* 4.1 24.9 - - + -
1370A LEU* 4.0 21.5 - - + -
1381A LEU* 4.3 7.9 - - + -
1385A VAL* 4.4 7.2 - - + -
1414A PHE* 5.5 2.2 - - + -
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Residues in contact with ASN1330 (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* 2.9 37.9 + - - +
1327A GLU* 3.2 11.1 + - - +
1329A LEU* 1.3 77.4 - - - +
1331A LEU* 1.3 61.8 + - + +
1333A PHE* 3.5 1.9 + - - +
1334A GLN* 3.1 44.7 + - - +
1367A ARG* 3.1 33.0 + - - +
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Residues in contact with LEU1331 (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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1327A GLU* 3.0 21.6 + - + +
1328A LEU* 3.2 16.1 + - + +
1330A ASN* 1.3 75.2 - - + +
1332A ILE* 1.3 67.1 + - - +
1334A GLN* 3.5 13.9 + - - +
1335A CYS* 3.4 21.0 + - - +
1413A PHE* 4.4 27.1 - - + -
1417A HIS* 6.0 4.0 - - + +
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Residues in contact with ILE1332 (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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1328A LEU* 3.0 27.2 + - + +
1329A LEU* 3.7 11.4 - - + +
1331A LEU* 1.3 75.4 - - - +
1333A PHE* 1.3 67.1 + - - +
1334A GLN 3.2 0.5 + - - -
1335A CYS* 3.3 15.2 + - - -
1338A SER* 2.9 23.6 + - - -
1363A PHE* 3.8 46.0 - - + -
1410A LEU* 3.9 17.9 - - + -
1413A PHE* 4.2 19.3 - - + -
1414A PHE* 4.0 34.1 - - + -
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Residues in contact with PHE1333 (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* 2.9 21.2 + - + +
1330A ASN* 3.8 4.9 - - - +
1331A LEU 3.3 0.2 - - - -
1332A ILE* 1.3 79.1 - - - +
1334A GLN* 1.3 59.9 + - + +
1338A SER* 3.1 6.3 + - - -
1342A ARG* 3.0 83.8 + - + -
1343A GLN* 4.2 8.1 - - - -
1363A PHE* 3.4 35.2 - + + -
1364A ALA* 3.6 12.6 - - + -
1367A ARG* 3.2 47.8 - - + +
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Residues in contact with GLN1334 (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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1330A ASN* 3.1 34.6 + - - +
1331A LEU* 4.1 13.7 - - - +
1332A ILE 3.2 0.8 - - - -
1333A PHE* 1.3 78.9 - - + +
1335A CYS* 1.3 59.8 + - - +
1336A GLU* 4.0 3.5 + - - +
1342A ARG* 4.3 3.4 + - - -
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Residues in contact with CYS1335 (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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1331A LEU 3.4 12.0 + - - +
1332A ILE* 3.3 14.7 + - - -
1333A PHE 3.2 0.6 - - - -
1334A GLN* 1.3 79.7 - - - +
1336A GLU* 1.3 61.4 + - - +
1337A ASP* 3.9 12.3 - - - +
1338A SER* 2.8 33.3 + - - -
1342A ARG* 2.9 4.3 + - - -
1410A LEU* 3.5 27.4 - - - -
1413A PHE* 6.0 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