Contacts of the helix formed by residues 505 - 512 (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 GLY 505 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501D GLU 4.5 6.0 + - - -
502D MET 3.8 9.2 + - - -
503D LEU 3.0 1.0 - - - -
504D ARG* 1.3 79.7 - - - +
506D MET* 1.3 60.6 + - - +
507D LYS* 3.1 4.2 + - - -
508D LEU* 3.3 7.9 + - - +
509D LEU* 2.9 28.1 + - - +
1430D VAL* 4.5 19.5 - - - +
1432D PHE* 6.1 2.9 - - - -
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Residues in contact with MET 506 (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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502D MET* 3.4 28.9 - - - +
503D LEU* 3.5 22.1 + - + +
504D ARG 3.8 0.2 - - - -
505D GLY* 1.3 77.5 - - - +
507D LYS* 1.3 57.4 + - - +
509D LEU* 3.5 20.9 - - + -
510D LYS* 2.9 57.4 + - + +
515D GLU* 5.1 0.2 - - - +
1105D ILE* 4.6 2.5 - - + +
1106D ILE* 3.9 22.0 - - + +
1110D MET* 4.2 3.6 - - + -
1113D PHE* 3.6 55.2 - - + -
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Residues in contact with LYS 507 (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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505D GLY* 3.1 2.1 - - - -
506D MET* 1.3 78.8 - - - +
508D LEU* 1.3 57.8 + - - +
510D LYS* 3.4 1.6 + - - +
511D LEU* 2.9 40.5 + - + +
1110D MET* 3.6 37.6 - - + +
1386D SER* 6.3 0.4 - - - -
1390D LEU* 3.7 41.0 - - + +
1395D MET* 4.6 1.3 - - + +
1426D LEU* 4.8 17.5 - - + +
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Residues in contact with LEU 508 (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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505D GLY* 3.3 6.9 + - - +
507D LYS* 1.3 79.5 - - - +
509D LEU* 1.3 66.7 + - + +
511D LEU* 3.4 20.4 + - - +
512D TYR* 3.2 43.1 - - + +
514D TRP* 4.6 2.5 - - + -
1426D LEU* 4.1 21.3 - - + -
1428D ASP 5.2 4.3 - - - +
1430D VAL* 3.7 38.1 - - + +
1432D PHE* 4.1 13.7 - - + -
1491D CYS* 5.0 7.6 - - + -
1494D ARG* 4.0 21.5 - - - +
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Residues in contact with LEU 509 (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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502D MET* 3.7 23.3 - - + +
505D GLY 2.9 18.3 + - - +
506D MET* 3.5 31.4 - - + +
507D LYS 3.2 0.2 - - - -
508D LEU* 1.3 81.8 - - - +
510D LYS* 1.3 57.8 + - - +
513D ALA* 3.0 22.9 + - - -
514D TRP* 3.2 35.7 + - + +
515D GLU* 4.1 23.2 - - + +
518D PHE* 3.6 36.6 - - + -
1106D ILE* 4.7 0.4 - - + -
1432D PHE* 5.7 3.4 - - + -
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Residues in contact with LYS 510 (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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506D MET* 2.9 43.3 + - + +
507D LYS* 5.2 0.2 - - - -
509D LEU* 1.3 70.3 - - - +
511D LEU* 1.3 66.7 + - - +
513D ALA* 3.7 5.4 + - - +
515D GLU* 3.1 29.4 + - + +
1106D ILE 2.7 27.9 + - - -
1107D LEU* 4.6 2.6 - - - +
1108D ALA 3.2 23.9 + - - +
1109D PRO* 4.9 3.4 - - - -
1110D MET* 4.6 13.0 - - + +
1113D PHE* 4.3 5.6 - - + -
1395D MET* 3.5 17.0 - - + +
1419D ARG* 3.2 31.4 + - - +
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Residues in contact with LEU 511 (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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507D LYS* 2.9 29.6 + - + +
508D LEU* 3.5 11.9 - - - +
509D LEU 3.2 1.2 - - - -
510D LYS* 1.3 75.8 - - - +
512D TYR* 1.3 63.2 + - + +
1390D LEU* 4.8 9.2 - - + -
1393D PHE* 3.4 27.3 - - + -
1395D MET* 3.7 33.0 - - + -
1419D ARG* 3.1 22.0 - - - -
1424D ILE* 3.8 21.8 - - + -
1426D LEU* 3.5 43.3 - - + -
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Residues in contact with TYR 512 (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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508D LEU* 3.2 46.1 + - + +
511D LEU* 1.3 76.4 - - + +
513D ALA* 1.3 70.7 + - - +
514D TRP* 3.5 47.8 + + - -
1393D PHE* 5.6 1.1 - - + -
1419D ARG 3.6 12.4 - - - +
1420D SER* 5.7 0.3 - - - -
1422D LEU 5.2 1.6 - - - +
1423D SER* 5.3 0.2 - - - -
1424D ILE* 3.6 40.5 + - + -
1426D LEU* 5.3 0.9 - - + -
1494D ARG* 3.4 24.0 - - + -
1498D ARG* 3.3 47.7 + - - +
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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