Contacts of the helix formed by residues 1483 - 1499 (chain B) in PDB entry 5TWV
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 SER1483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1481B ASN 4.1 0.6 + - - -
1482B PHE* 1.3 77.2 - - - +
1484B GLN* 1.3 60.2 + - - +
1485B GLY* 3.3 5.3 + - - -
1486B GLN* 2.9 27.1 + - - +
1487B ARG* 2.9 27.9 + - - +
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Residues in contact with GLN1484 (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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1427B GLN 4.5 9.2 - - - +
1429B PRO* 6.3 0.2 - - - -
1482B PHE 4.0 0.2 + - - -
1483B SER* 1.3 74.1 - - - +
1485B GLY* 1.3 58.3 + - - +
1487B ARG* 3.6 6.3 - - - +
1488B GLN* 2.9 27.4 + - - +
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Residues in contact with GLY1485 (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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1483B SER* 3.2 5.5 + - - -
1484B GLN* 1.3 77.6 - - - +
1486B GLN* 1.3 60.1 + - - +
1488B GLN* 3.1 8.6 + - - +
1489B LEU* 2.9 28.2 + - - +
1512B ILE* 5.8 9.0 - - - +
1516B THR* 6.3 3.1 - - - -
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Residues in contact with GLN1486 (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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1463B VAL* 5.0 16.4 - - + -
1482B PHE* 4.2 9.9 - - + -
1483B SER* 2.9 28.0 + - - +
1485B GLY* 1.3 74.2 - - - +
1487B ARG* 1.3 57.9 + - - +
1489B LEU* 3.4 8.2 + - - +
1490B PHE* 2.9 28.3 + - - +
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Residues in contact with ARG1487 (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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1429B PRO* 3.3 33.2 - - + +
1479B GLY 5.3 4.9 - - - +
1482B PHE* 4.4 9.3 - - + +
1483B SER 2.9 18.6 + - - +
1484B GLN* 3.6 7.4 - - - +
1486B GLN* 1.3 76.5 - - - +
1488B GLN* 1.3 58.2 + - - +
1490B PHE* 3.3 8.5 + - - +
1491B CYS 2.9 24.3 + - - -
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Residues in contact with GLN1488 (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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1425B ILE* 5.3 0.7 - - - +
1426B LEU 4.9 4.9 - - - +
1427B GLN* 4.6 14.1 - - - +
1429B PRO* 4.4 0.8 - - - +
1484B GLN 2.9 14.7 + - - +
1485B GLY* 3.1 13.0 + - - +
1487B ARG* 1.3 73.1 - - - +
1489B LEU* 1.3 59.7 + - - +
1491B CYS* 3.4 7.8 + - - +
1492B LEU* 2.9 27.7 + - - +
1520B LEU* 6.3 4.0 - - + -
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Residues in contact with LEU1489 (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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1458B ALA 4.5 5.5 - - - +
1459B GLN 5.0 3.4 - - - +
1460B LEU* 4.3 22.1 - - + +
1485B GLY 2.9 12.4 + - - +
1486B GLN* 3.6 11.7 - - - +
1488B GLN* 1.3 71.9 - - - +
1490B PHE* 1.3 61.3 + - - +
1492B LEU* 3.2 7.6 + - - +
1493B ALA* 2.9 29.8 + - - +
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Residues in contact with PHE1490 (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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1429B PRO* 6.0 0.4 - - + -
1440B LEU* 5.9 2.5 - - + +
1460B LEU* 4.9 4.4 - - - +
1486B GLN 2.9 18.1 + - - +
1487B ARG* 3.5 10.3 - - - +
1488B GLN 3.3 0.2 - - - -
1489B LEU* 1.3 75.1 - - - +
1491B CYS* 1.3 58.0 + - - +
1493B ALA* 3.4 7.3 + - - +
1494B ARG* 2.9 28.6 + - - +
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Residues in contact with CYS1491 (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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1424B ILE 4.7 2.8 - - - +
1425B ILE* 3.5 30.7 - - + +
1426B LEU 4.4 6.1 - - - +
1429B PRO* 3.9 22.4 - - + -
1487B ARG 2.9 17.2 + - - +
1488B GLN 3.6 5.6 - - - +
1490B PHE* 1.3 75.9 - - - +
1492B LEU* 1.3 57.8 + - - +
1494B ARG* 3.3 9.4 + - - +
1495B ALA 2.9 23.0 + - - -
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Residues in contact with LEU1492 (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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1425B ILE* 4.1 9.3 - - + +
1458B ALA* 4.6 7.4 - - + +
1488B GLN 2.9 15.1 + - - +
1489B LEU* 3.2 11.4 + - - +
1491B CYS* 1.3 75.7 - - - +
1493B ALA* 1.3 57.8 + - - +
1495B ALA* 3.2 6.5 + - - +
1496B PHE* 2.9 27.1 + - - +
1523B VAL* 5.8 7.9 - - + -
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Residues in contact with ALA1493 (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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1451B LEU 5.7 0.7 - - - +
1454B ALA* 4.6 3.1 - - + +
1455B LEU* 4.2 22.9 - - + +
1458B ALA* 3.8 24.6 - - + +
1460B LEU* 4.6 3.6 - - + -
1489B LEU 2.9 16.9 + - - +
1490B PHE* 3.7 7.0 - - - +
1492B LEU* 1.3 75.2 - - - +
1494B ARG* 1.3 54.6 + - - +
1496B PHE* 3.1 2.5 + - - +
1497B VAL* 2.7 37.3 + - - +
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Residues in contact with ARG1494 (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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1423B SER* 4.8 0.7 - - - -
1424B ILE 5.8 2.7 - - - +
1439B ASN 6.0 0.4 - - - +
1440B LEU* 5.6 11.6 - - + +
1442B PRO* 5.1 18.0 - - + +
1490B PHE 2.9 17.5 + - - +
1491B CYS* 3.4 11.0 - - - +
1493B ALA* 1.3 77.4 - - - +
1495B ALA* 1.3 58.8 + - - +
1497B VAL* 3.8 7.2 + - - +
1498B ARG* 3.4 20.6 + - - +
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Residues in contact with ALA1495 (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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1423B SER* 3.7 26.6 - - - +
1424B ILE 5.1 1.5 + - - -
1425B ILE* 4.5 11.9 - - + +
1491B CYS 2.9 13.9 + - - +
1492B LEU* 3.2 11.6 + - - +
1494B ARG* 1.3 75.7 - - - +
1496B PHE* 1.3 63.7 + - - +
1498B ARG* 3.2 12.1 + - - +
1499B LYS 3.4 8.3 + - - -
1500B THR* 3.9 9.0 + - - -
1503B PHE* 6.1 4.7 - - + -
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Residues in contact with PHE1496 (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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1454B ALA* 3.7 30.5 - - + -
1457B ILE* 3.6 30.3 - - + -
1458B ALA* 4.3 10.3 - - + -
1492B LEU 2.9 13.6 + - - +
1493B ALA* 3.1 11.0 + - - +
1495B ALA* 1.3 75.8 - - - +
1497B VAL* 1.3 61.8 + - - +
1499B LYS* 3.2 16.3 + - - +
1531B ARG* 4.2 28.7 + - - +
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Residues in contact with VAL1497 (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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1440B LEU 5.5 6.5 - - - +
1443B GLU* 5.2 9.3 - - + +
1451B LEU* 5.4 9.4 - - + -
1454B ALA* 4.4 17.0 - - + -
1493B ALA 2.7 19.5 + - - +
1494B ARG* 4.1 7.2 - - - +
1495B ALA 3.3 0.2 - - - -
1496B PHE* 1.3 74.3 - - - +
1498B ARG* 1.3 60.1 + - - +
1499B LYS* 3.5 3.6 + - - +
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Residues in contact with ARG1498 (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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1420B SER 5.7 5.2 - - - +
1421B ARG 5.6 2.8 - - - +
1422B LEU 5.9 0.4 - - - -
1423B SER* 4.1 17.5 - - - +
1443B GLU* 5.3 11.2 - - + -
1494B ARG 3.4 14.4 + - - +
1495B ALA 3.2 6.5 + - - +
1496B PHE 3.2 1.0 - - - -
1497B VAL* 1.3 77.2 - - - +
1499B LYS* 1.3 69.8 + - - +
1500B THR* 3.3 2.6 + - - +
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Residues in contact with LYS1499 (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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1495B ALA 3.4 1.6 + - - -
1496B PHE* 3.2 17.3 + - - +
1497B VAL 4.5 3.6 - - - +
1498B ARG* 1.3 79.3 - - - +
1500B THR* 1.3 67.5 + - - +
1501B SER 3.8 0.2 + - - -
1531B ARG* 4.5 12.3 - - - +
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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