Contacts of the helix formed by residues 564 - 571 (chain B) in PDB entry 1PTH
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 LEU 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B MET* 4.5 7.4 - - + -
201B PHE* 4.4 6.1 - - + -
301B TYR* 4.4 13.2 - - + +
343B ILE* 3.9 11.3 - - + +
347B GLU* 3.0 26.2 + - - +
563B THR* 1.3 70.2 - - - +
565B LYS* 1.3 63.3 + - - +
567B LEU* 3.1 21.7 - - + +
568B VAL* 3.1 34.4 + - + +
578B VAL* 4.1 11.7 - - + +
579B SER* 3.9 31.2 - - - +
580B PHE* 3.6 38.6 - - + +
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Residues in contact with LYS 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU* 4.1 0.4 + - - +
563B THR* 3.0 14.3 - - + +
564B LEU* 1.3 77.1 - - - +
566B LYS* 1.3 63.8 + - + +
568B VAL 3.3 0.2 + - - -
569B CYS* 2.8 42.6 + - + +
575B CYS* 3.4 23.2 - - - -
576B PRO 4.0 5.1 + - - -
577B TYR* 5.6 0.4 - - - +
578B VAL* 3.5 36.8 - - + +
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Residues in contact with LYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 5.8 2.2 - - - +
558B LEU* 5.6 2.0 + - - +
561B THR* 3.1 34.8 + - - +
562B ALA* 5.1 1.9 - - - +
563B THR* 3.0 33.4 + - + +
565B LYS* 1.3 79.1 - - + +
567B LEU* 1.3 63.9 + - - +
569B CYS* 5.0 0.4 - - - -
570B LEU* 2.9 57.6 + - + +
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Residues in contact with LEU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 4.9 3.8 - - + -
301B TYR* 5.4 3.8 - - + -
304B ILE* 3.5 25.0 - - + +
305B TRP* 3.3 60.1 - - + +
308B GLU* 4.1 19.7 - - + -
339B GLU* 5.7 2.5 - - - +
343B ILE* 3.7 15.0 - - + -
563B THR 2.7 15.7 + - - +
564B LEU* 3.1 23.1 - - + +
566B LYS* 1.3 73.3 - - - +
568B VAL* 1.3 62.0 + - + +
571B ASN* 2.9 28.4 + - - +
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 4.3 11.7 - - + -
304B ILE* 4.1 25.6 - - + -
419B VAL* 4.3 0.4 - - + -
420B GLU* 5.4 0.2 - - - -
423B VAL* 3.9 22.7 - - + -
564B LEU* 3.1 21.2 + - + +
565B LYS 4.0 1.1 - - - +
567B LEU* 1.3 76.7 - - + +
569B CYS* 1.3 55.7 + - - +
571B ASN* 2.7 29.1 + - - +
572B THR* 3.0 28.3 + - + +
576B PRO* 4.5 5.8 - - + -
578B VAL* 3.8 28.9 - - + -
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Residues in contact with CYS 569 (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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565B LYS* 2.8 28.7 + - + +
568B VAL* 1.3 74.8 - - - +
570B LEU* 1.3 65.9 + - + +
572B THR* 3.3 23.5 - - - +
575B CYS* 2.0 59.7 + - + +
576B PRO* 3.6 11.4 - - - -
578B VAL* 4.3 6.7 - - - -
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Residues in contact with LEU 570 (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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308B GLU* 5.4 0.2 - - - +
311B ARG* 3.4 45.8 - - - +
566B LYS* 2.9 61.8 + - + +
569B CYS* 1.3 78.5 - - + +
571B ASN* 1.3 66.5 + - - +
572B THR 3.4 1.6 + - - +
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Residues in contact with ASN 571 (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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261B VAL* 5.9 0.2 - - - +
304B ILE* 3.9 8.3 + - + +
307B ARG* 2.9 48.6 + - + +
308B GLU* 3.1 41.0 + - - +
311B ARG* 3.5 21.1 - - - +
567B LEU* 2.9 21.3 + - - +
568B VAL 2.7 7.4 + - - +
570B LEU* 1.3 86.2 - - - +
572B THR* 1.3 59.4 + - + +
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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