Contacts of the helix formed by residues 1449 - 1461 (chain B) in PDB entry 4C29
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 GLN1449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1438B PHE* 4.4 13.9 - - - -
1439B VAL 4.7 5.0 + - - +
1440B LEU* 3.9 32.9 - - + +
1445B GLU* 3.3 25.0 + - - +
1446B LEU 3.2 6.0 + - - +
1448B GLN* 1.3 82.0 - - + +
1450B ARG* 1.3 64.1 + - - +
1451B ASP 3.4 2.0 - - - -
1452B GLU* 3.4 28.5 + - - +
1453B ILE* 3.0 33.0 + - + +
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Residues in contact with ARG1450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299B PHE* 4.3 14.1 - - + -
1302B ASP* 3.6 29.7 + - + +
1303B MET* 4.3 17.5 - - - +
1306B ARG* 3.0 53.1 - - - +
1446B LEU 3.0 10.9 + - - +
1447B GLU* 3.2 47.3 + - - +
1448B GLN 3.4 1.8 - - - -
1449B GLN* 1.3 78.1 - - - +
1451B ASP* 1.3 79.9 + - - +
1453B ILE* 3.3 1.4 + - - +
1454B VAL* 3.0 32.1 + - + +
2469B PEG 5.3 2.0 + - - -
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Residues in contact with ASP1451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268B HIS* 4.7 15.2 + - - +
1306B ARG* 3.9 12.8 + - - -
1447B GLU 5.0 0.2 + - - -
1448B GLN 5.0 2.8 + - - +
1449B GLN 3.4 0.4 - - - -
1450B ARG* 1.3 101.5 + - - +
1452B GLU* 1.3 60.3 + - - +
1454B VAL* 3.3 7.5 - - - +
1455B SER* 2.8 31.9 + - - +
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Residues in contact with GLU1452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436B LYS* 5.1 3.5 + - - -
1438B PHE* 4.3 19.9 - - + -
1448B GLN 5.5 1.3 + - - +
1449B GLN* 3.4 35.3 + - - +
1450B ARG 3.3 0.6 - - - -
1451B ASP* 1.3 80.2 - - - +
1453B ILE* 1.3 63.0 + - - +
1455B SER* 3.8 4.2 - - - -
1456B TYR* 3.1 22.7 + - + +
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Residues in contact with ILE1453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299B PHE* 4.3 28.9 - - + -
1303B MET* 4.9 2.0 - - + -
1382B LEU* 4.9 9.2 - - + -
1414B VAL* 5.2 6.1 - - + -
1438B PHE* 3.9 50.5 - - + -
1440B LEU* 5.1 4.0 - - + -
1446B LEU* 5.1 9.0 - - + -
1449B GLN* 3.0 30.9 + - + +
1450B ARG* 3.9 3.6 - - - +
1452B GLU* 1.3 74.6 - - + +
1454B VAL* 1.3 60.4 + - - +
1456B TYR* 3.1 4.2 + - - +
1457B LEU* 2.9 49.9 + - + +
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Residues in contact with VAL1454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268B HIS* 4.2 20.9 - - + +
1271B CYS* 3.7 18.2 - - + -
1303B MET* 4.0 21.8 - - + +
1306B ARG* 5.2 11.7 - - + -
1307B LEU* 4.1 19.1 - - + -
1450B ARG* 3.0 24.1 + - + +
1451B ASP* 3.3 16.6 - - - +
1453B ILE* 1.3 77.0 - - - +
1455B SER* 1.3 65.3 + - - +
1457B LEU* 3.3 10.5 + - + +
1458B CYS* 3.1 24.9 + - - -
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Residues in contact with SER1455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268B HIS* 3.2 22.1 + - - -
1270B PHE* 3.2 29.2 - - - +
1271B CYS* 4.7 0.2 - - - -
1451B ASP* 2.8 20.3 + - - +
1452B GLU* 3.8 4.7 - - - -
1454B VAL* 1.3 79.2 - - - +
1456B TYR* 1.3 61.7 + - - +
1458B CYS 3.5 0.2 + - - -
1459B ASP* 3.0 22.1 + - - +
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Residues in contact with TYR1456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412B ILE* 4.0 18.4 - - + -
1433B PRO 3.6 7.3 + - - -
1434B GLU* 3.1 21.8 + - - -
1436B LYS* 3.1 38.7 - - + +
1438B PHE* 4.1 24.9 - + + -
1452B GLU* 3.1 15.8 + - + +
1453B ILE 3.1 8.3 + - - +
1455B SER* 1.3 78.0 - - - +
1457B LEU* 1.3 66.3 + - + +
1459B ASP* 3.4 15.3 + - + +
1460B LEU* 3.5 36.9 + - + +
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Residues in contact with LEU1457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B LEU* 4.8 7.6 - - + +
1278B LEU* 4.1 21.5 - - + -
1303B MET* 3.6 31.0 - - + -
1380B ILE* 3.6 25.2 - - + +
1382B LEU* 4.4 14.6 - - + -
1412B ILE* 3.5 31.2 - - + -
1453B ILE* 2.9 28.3 + - + +
1454B VAL* 3.6 7.6 - - + +
1455B SER 3.3 0.2 - - - -
1456B TYR* 1.3 81.2 - - + +
1458B CYS* 1.3 64.7 + - - +
1460B LEU* 3.1 20.2 + - - +
1461B ALA* 3.5 4.7 + - - +
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Residues in contact with CYS1458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B PHE* 4.1 3.6 - - + -
1271B CYS* 2.0 53.2 - - - -
1274B ARG* 3.1 34.4 + - - +
1276B LEU* 4.8 9.9 - - - -
1307B LEU* 4.2 11.4 - - - -
1314B VAL* 6.0 0.4 - - - -
1454B VAL* 3.1 7.7 + - - +
1455B SER 4.1 3.1 - - - +
1457B LEU* 1.3 78.8 - - - +
1459B ASP* 1.3 59.1 + - - +
1461B ALA* 2.9 32.1 + - - +
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Residues in contact with ASP1459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B PHE* 3.8 22.1 - - + -
1274B ARG* 4.4 6.2 + - - +
1455B SER 3.0 18.2 + - - +
1456B TYR* 3.6 11.7 - - + +
1457B LEU 3.2 0.8 - - - -
1458B CYS* 1.3 76.9 - - - +
1460B LEU* 1.3 63.1 + - + +
1461B ALA 3.5 4.5 + - - +
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Residues in contact with LEU1460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378B SER* 3.0 14.8 + - - -
1380B ILE* 4.0 16.2 - - + -
1410B ILE* 3.8 33.0 - - + +
1412B ILE* 4.0 9.4 - - + -
1434B GLU* 4.3 22.2 - - + +
1456B TYR* 3.5 43.5 - - + +
1457B LEU* 3.1 6.5 + - - +
1458B CYS 3.1 0.4 - - - -
1459B ASP* 1.3 81.8 - - + +
1461B ALA* 1.3 59.9 + - - +
1462B PRO* 4.0 0.9 - - - +
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Residues in contact with ALA1461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274B ARG* 2.9 38.9 + - + -
1275B LEU 3.7 13.9 - - - +
1276B LEU* 4.0 15.0 - - + -
1378B SER* 3.4 9.0 - - - -
1457B LEU 3.5 4.9 + - - +
1458B CYS* 2.9 14.3 + - - +
1459B ASP 3.9 2.8 - - - +
1460B LEU* 1.3 80.7 - - - +
1462B PRO* 1.3 69.0 - - + +
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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