Contacts of the helix formed by residues 505 - 512 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B GLU 4.5 6.4 + - - -
502B MET 3.8 9.4 + - - -
503B LEU 3.0 0.8 - - - -
504B ARG* 1.3 79.9 - - - +
506B MET* 1.3 58.0 + - - +
507B LYS* 3.1 4.8 + - - -
508B LEU* 3.3 7.9 + - - +
509B LEU* 2.9 28.1 + - - +
1430B VAL* 4.5 19.5 - - - -
1432B PHE* 6.1 3.7 - - - -
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Residues in contact with MET 506 (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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502B MET* 3.4 30.1 - - - +
503B LEU* 3.5 21.1 + - + +
504B ARG 3.8 0.4 - - - -
505B GLY* 1.3 78.1 - - - +
507B LYS* 1.3 57.0 + - - +
509B LEU* 3.5 19.7 - - + -
510B LYS* 2.9 56.4 + - + +
515B GLU* 5.1 0.4 - - - +
1105B ILE* 4.6 1.6 - - + +
1106B ILE* 3.9 21.8 - - + +
1110B MET* 4.2 3.1 - - + -
1113B PHE* 3.6 55.9 - - + -
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Residues in contact with LYS 507 (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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505B GLY* 3.1 1.3 - - - -
506B MET* 1.3 80.0 - - - +
508B LEU* 1.3 58.4 + - - +
510B LYS* 3.8 1.6 - - - +
511B LEU* 2.9 41.0 + - + +
1110B MET* 3.6 37.4 - - + +
1386B SER* 6.3 0.4 - - - -
1390B LEU* 3.7 39.6 - - + +
1395B MET* 4.6 0.6 - - + +
1426B LEU* 4.8 16.2 - - + +
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Residues in contact with LEU 508 (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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505B GLY* 3.3 6.8 + - - +
507B LYS* 1.3 79.9 - - - +
509B LEU* 1.3 64.7 + - - +
511B LEU* 3.4 20.9 + - - +
512B TYR* 3.2 41.7 - - + +
514B TRP* 4.6 2.0 - - + -
1426B LEU* 4.1 21.8 - - + -
1428B ASP 5.2 3.6 - - - +
1430B VAL* 3.7 39.0 - - + +
1432B PHE* 4.1 13.7 - - + -
1491B CYS* 5.0 7.0 - - + -
1494B ARG* 4.0 22.2 - - - +
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Residues in contact with LEU 509 (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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502B MET* 3.7 22.9 - - + +
505B GLY 2.9 19.4 + - - +
506B MET* 3.5 31.4 - - + +
507B LYS 3.2 0.2 - - - -
508B LEU* 1.3 81.9 - - - +
510B LYS* 1.3 56.5 + - - +
513B ALA* 3.0 23.0 + - - -
514B TRP* 3.2 35.4 + - + +
515B GLU* 4.1 24.0 - - + +
518B PHE* 3.6 36.6 - - + -
1106B ILE* 4.7 0.4 - - + -
1432B PHE* 5.7 3.4 - - + -
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Residues in contact with LYS 510 (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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506B MET* 2.9 44.2 + - + +
507B LYS* 4.1 0.4 - - - +
509B LEU* 1.3 71.2 - - - +
511B LEU* 1.3 66.2 + - - +
512B TYR 3.5 0.2 - - - -
513B ALA* 3.7 5.2 + - - +
515B GLU* 3.1 28.9 + - - +
1106B ILE 2.7 27.7 + - - -
1107B LEU* 4.6 2.6 - - - +
1108B ALA 3.2 23.1 + - - +
1109B PRO* 4.9 4.3 - - - -
1110B MET* 4.6 12.3 - - + +
1113B PHE* 4.3 5.8 - - + -
1395B MET* 3.7 15.7 - - + -
1419B ARG* 3.2 31.8 + - - +
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Residues in contact with LEU 511 (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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507B LYS* 2.9 29.7 + - + +
508B LEU* 3.5 12.1 - - - +
509B LEU 3.2 1.2 - - - -
510B LYS* 1.3 75.0 - - - +
512B TYR* 1.3 63.0 + - + +
1390B LEU* 4.8 9.2 - - + -
1393B PHE* 3.4 27.7 - - + -
1395B MET* 3.7 31.6 - - + -
1419B ARG* 3.1 21.7 - - - -
1424B ILE* 3.8 20.4 - - + -
1426B LEU* 3.5 43.7 - - + -
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Residues in contact with TYR 512 (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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508B LEU* 3.2 45.9 + - + +
511B LEU* 1.3 75.7 - - + +
513B ALA* 1.3 71.8 + - - +
514B TRP* 3.5 47.9 + + - -
1393B PHE* 5.6 0.9 - - + -
1419B ARG 3.6 13.4 - - - +
1422B LEU 5.2 1.3 - - - +
1423B SER* 5.3 0.2 - - - -
1424B ILE* 3.6 41.0 + - + -
1426B LEU* 5.3 1.1 - - + -
1494B ARG* 3.4 23.7 - - + -
1498B ARG* 3.3 49.2 + - - +
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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