Contacts of the helix formed by residues 1539 - 1546 (chain D) in PDB entry 5YWB
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 ARG1539 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889D HIS* 4.4 6.9 + - - -
890D LYS* 3.5 32.7 - - - +
1509D THR* 3.3 39.4 + - + +
1512D ILE 3.5 15.2 + - - -
1514D MET* 3.3 46.8 - - - +
1517D GLU* 4.6 5.6 - - - +
1518D ASN* 5.5 5.8 - - - +
1537D ALA 3.1 1.6 - - - -
1538D HIS* 1.3 94.4 + - - +
1540D VAL* 1.3 64.8 + - - +
1541D HIS* 4.2 11.9 - - + +
1542D THR* 2.9 33.9 + - + +
1543D ILE* 3.2 15.1 - - - +
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Residues in contact with VAL1540 (chain D).
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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862D VAL* 4.9 14.4 - - + -
1538D HIS 5.1 0.2 - - - +
1539D ARG* 1.3 75.5 - - - +
1541D HIS* 1.3 61.5 + - - +
1543D ILE* 3.2 10.3 + - + +
1544D LEU* 2.9 29.2 + - + +
1575D ALA 5.5 1.1 - - - +
1578D VAL* 3.9 26.7 - - + +
1579D ARG* 3.6 36.1 - - + +
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Residues in contact with HIS1541 (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* 3.5 29.6 + - + +
1522D LYS* 6.2 1.8 - - - -
1539D ARG* 3.4 7.4 - - + +
1540D VAL* 1.3 80.0 - - - +
1542D THR* 1.3 62.7 + - - +
1544D LEU* 2.9 38.5 + - + +
1545D SER* 3.0 20.6 + - - -
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Residues in contact with THR1542 (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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1509D THR* 4.9 3.6 - - - +
1517D GLU* 4.4 11.2 - - + +
1518D ASN* 5.2 8.1 - - - +
1521D GLN* 3.8 34.5 - - + +
1525D MET* 6.0 1.9 - - - +
1535D THR* 5.4 6.1 + - - -
1537D ALA* 3.5 15.7 - - + +
1539D ARG* 2.9 37.2 + - + +
1541D HIS* 1.3 76.9 - - - +
1543D ILE* 1.3 61.5 + - - +
1544D LEU 3.3 0.3 + - - -
1545D SER* 3.3 15.2 + - - -
1546D ALA* 3.8 9.0 + - - +
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Residues in contact with ILE1543 (chain D).
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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1376D GLY* 5.0 2.0 - - - -
1377D ILE 3.3 31.6 - - - +
1378D CYS* 4.1 25.4 - - + -
1535D THR* 4.9 7.6 - - - +
1537D ALA* 3.6 24.5 - - + +
1539D ARG 3.2 17.0 - - - +
1540D VAL* 3.2 10.0 + - + +
1542D THR* 1.3 78.7 + - - +
1544D LEU* 1.3 62.9 + - - +
1546D ALA* 3.4 10.5 + - - +
1549D VAL* 3.5 31.0 - - + +
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Residues in contact with LEU1544 (chain D).
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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1540D VAL* 2.9 17.5 + - + +
1541D HIS* 2.9 34.3 + - + +
1543D ILE* 1.3 78.6 - - - +
1545D SER* 1.3 63.7 + - - +
1546D ALA 3.1 8.1 + - - +
1563D PRO* 5.3 17.1 - - + +
1567D LEU* 5.2 15.0 - - + -
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Residues in contact with SER1545 (chain D).
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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1525D MET* 5.7 7.5 - - - +
1541D HIS* 3.0 20.5 + - - -
1542D THR* 3.3 8.3 + - - -
1543D ILE 3.3 0.8 - - - -
1544D LEU* 1.3 78.0 - - - +
1546D ALA* 1.3 60.4 + - - +
1547D ASP* 4.3 5.9 - - - +
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Residues in contact with ALA1546 (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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1374D LYS* 4.5 14.6 - - + +
1375D ILE 4.7 1.6 - - - -
1376D GLY* 4.1 17.7 - - - +
1525D MET* 6.5 0.9 - - + -
1535D THR* 5.7 1.8 - - - +
1542D THR 3.8 6.8 + - - +
1543D ILE* 3.4 13.3 + - - +
1544D LEU 3.1 10.1 - - - +
1545D SER* 1.3 82.3 - - - +
1547D ASP* 1.3 66.4 + - - +
1548D LEU 4.7 0.2 - - - +
1549D VAL* 3.7 18.5 - - + +
1563D PRO* 4.9 8.5 - - - +
1566D LEU* 5.7 2.1 - - - +
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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