Contacts of the helix formed by residues 1514 - 1529 (chain D) 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 MET1514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1513D ASP* 1.3 74.4 - - - +
1515D ALA* 1.3 54.9 + - - +
1516D THR 3.2 0.2 - - - -
1517D GLU* 5.1 0.2 - - - -
1518D ASN* 2.7 41.4 + - - +
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Residues in contact with ALA1515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513D ASP* 4.3 2.6 - - + +
1514D MET* 1.3 77.8 - - - +
1516D THR* 1.3 56.9 + - - +
1518D ASN* 4.0 3.7 - - - +
1519D ILE* 3.0 27.7 + - - +
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Residues in contact with THR1516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485D GLY* 6.3 3.4 - - - -
1512D ILE* 4.5 9.9 - - - -
1513D ASP* 3.7 19.8 - - - +
1514D MET 3.2 0.2 - - - -
1515D ALA* 1.3 79.4 - - - +
1517D GLU* 1.3 62.5 + - - +
1519D ILE* 3.7 5.8 - - - +
1520D LEU* 2.8 28.6 + - - +
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Residues in contact with GLU1517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511D SER* 6.1 0.9 - - - -
1512D ILE* 4.4 12.5 - - + +
1513D ASP 3.2 27.1 + - - +
1514D MET* 4.6 0.4 - - - +
1516D THR* 1.3 77.7 - - - +
1518D ASN* 1.3 57.5 + - - +
1520D LEU* 3.3 7.6 + - - +
1521D GLN* 2.9 30.5 + - - +
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Residues in contact with ASN1518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514D MET 2.7 24.3 + - - +
1515D ALA* 4.0 4.7 - - - +
1517D GLU* 1.3 74.6 - - - +
1519D ILE* 1.3 59.8 + - - +
1521D GLN* 3.5 6.4 + - - +
1522D LYS* 3.0 26.2 + - - +
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Residues in contact with ILE1519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515D ALA 3.0 23.1 + - - +
1516D THR* 3.7 6.5 - - - +
1518D ASN* 1.3 75.5 - - - +
1520D LEU* 1.3 54.5 + - - +
1522D LYS* 3.1 9.5 + - - +
1523D VAL* 2.8 34.8 + - - +
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Residues in contact with LEU1520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488D GLN* 6.3 3.1 - - + -
1516D THR 2.8 21.5 + - - +
1517D GLU* 3.4 10.1 - - - +
1519D ILE* 1.3 72.5 - - - +
1521D GLN* 1.3 57.6 + - - +
1523D VAL* 3.3 9.2 + - - +
1524D VAL* 2.8 27.9 + - - +
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Residues in contact with GLN1521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517D GLU 2.9 17.6 + - - +
1518D ASN* 3.7 7.4 - - - +
1520D LEU* 1.3 73.5 - - - +
1522D LYS* 1.3 59.0 + - - +
1524D VAL* 3.3 8.5 + - - +
1525D MET* 2.9 28.6 + - - +
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Residues in contact with LYS1522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518D ASN 3.0 15.3 + - - +
1519D ILE* 3.1 12.1 + - - +
1521D GLN* 1.3 75.5 - - - +
1523D VAL* 1.3 58.0 + - - +
1525D MET* 3.3 8.6 + - - +
1526D THR* 2.9 28.9 + - - -
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Residues in contact with VAL1523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459D GLN* 6.2 4.7 - - + -
1492D LEU* 5.8 7.9 - - + -
1519D ILE 2.8 15.5 + - - +
1520D LEU* 3.4 13.2 - - - +
1522D LYS* 1.3 68.7 - - - +
1524D VAL* 1.3 60.9 + - - +
1526D THR* 3.8 6.2 - - - +
1527D ALA* 2.8 31.2 + - - +
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Residues in contact with VAL1524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1520D LEU 2.8 16.7 + - - +
1521D GLN* 3.6 10.5 - - - +
1523D VAL* 1.3 76.7 - - - +
1525D MET* 1.3 56.4 + - - +
1527D ALA* 3.7 5.4 - - - +
1528D PHE* 2.8 32.7 + - - +
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Residues in contact with MET1525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521D GLN 2.9 17.2 + - - +
1522D LYS* 3.3 8.7 + - - +
1524D VAL* 1.3 76.4 - - - +
1526D THR* 1.3 56.4 + - - +
1528D PHE* 3.5 3.9 + - - +
1529D ALA* 2.9 28.6 + - - +
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Residues in contact with THR1526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1522D LYS 2.9 16.7 + - - -
1523D VAL* 3.9 5.8 - - - -
1525D MET* 1.3 72.4 - - - +
1527D ALA* 1.3 66.9 + - - +
1529D ALA* 3.3 21.6 + - - +
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Residues in contact with ALA1527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492D LEU* 6.5 1.3 - - + -
1523D VAL 2.8 21.9 + - - +
1524D VAL* 3.7 7.9 - - - +
1526D THR* 1.3 73.7 - - - +
1528D PHE* 1.3 62.5 + - - +
1529D ALA 3.4 1.2 + - - +
1531D ARG* 3.5 34.7 + - - +
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Residues in contact with PHE1528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372D GLY 3.7 8.8 - - - +
1374D LYS* 4.7 13.5 - - + -
1503D PHE* 6.2 1.3 - - - -
1524D VAL 2.8 22.6 + - - +
1525D MET* 4.1 4.3 - - - +
1527D ALA* 1.3 70.5 - - - +
1529D ALA* 1.3 63.8 + - - +
1530D ASP 3.1 1.2 + - - -
1531D ARG* 2.9 27.3 + - - +
1533D VAL* 3.7 28.5 - - + -
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Residues in contact with ALA1529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372D GLY 5.3 0.4 - - - -
1525D MET 2.9 15.4 + - - +
1526D THR* 3.4 18.7 - - - +
1527D ALA 3.2 7.9 - - - +
1528D PHE* 1.3 74.1 - - - +
1530D ASP* 1.3 65.2 + - + +
1531D ARG* 3.2 8.4 + - - +
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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