Contacts of the helix formed by residues 560 - 573 (chain B) in PDB entry 3THW
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 THR 560 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558B THR* 3.8 8.5 + - - -
559B LYS* 1.3 79.5 - - - +
561B SER* 1.3 62.9 + - - +
562B PHE* 3.4 35.4 - - + -
563B GLY* 3.0 26.9 + - - -
564B ARG* 3.5 12.8 + - - +
606B LEU* 3.3 41.3 - - + +
609B LEU* 4.0 11.7 - - + -
610B PRO 4.5 4.0 - - - -
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Residues in contact with SER 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASN* 5.6 1.9 + - - -
349B GLU* 5.8 7.2 - - - -
560B THR* 1.3 70.1 - - - +
562B PHE* 1.3 61.0 + - - +
563B GLY 3.0 5.6 + - - -
564B ARG* 3.3 27.4 + - - +
565B ARG* 3.3 23.3 + - - +
610B PRO 3.6 4.1 + - - -
611B ASP* 3.0 44.1 + - - +
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Residues in contact with PHE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B THR* 3.4 29.2 - - + -
561B SER* 1.3 77.0 - - - +
563B GLY* 1.3 62.1 + - - +
565B ARG* 3.4 27.0 - - - +
566B LYS* 3.5 20.1 + - - +
609B LEU* 4.5 9.0 - - + -
610B PRO 3.4 25.6 - - - -
611B ASP* 4.1 4.7 - - - -
612B ILE* 3.8 35.2 - - + -
613B GLU* 3.5 21.6 - - + +
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Residues in contact with GLY 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B THR* 3.7 17.4 - - - +
560B THR* 3.0 21.5 + - - -
561B SER 3.0 0.4 - - - -
562B PHE* 1.3 79.4 - - - +
564B ARG* 1.3 65.8 + - - +
566B LYS* 3.2 7.7 + - - +
567B LEU* 3.1 17.8 + - - +
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Residues in contact with ARG 564 (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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349B GLU* 5.1 9.3 + - - -
355B SER* 4.1 24.9 - - - -
552B LEU* 5.4 9.9 - - + +
556B ASP* 3.1 31.1 + - - +
558B THR* 3.3 33.2 + - - +
559B LYS 6.3 0.2 - - - -
560B THR 3.5 7.5 + - - +
561B SER* 3.3 25.2 + - - +
563B GLY* 1.3 75.8 - - - +
565B ARG* 1.3 64.3 + - - +
567B LEU* 3.2 5.6 + - + +
568B LYS* 3.1 22.9 + - + +
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Residues in contact with ARG 565 (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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350B ILE* 4.1 18.3 - - - +
355B SER* 3.4 29.8 + - - +
356B THR* 3.9 17.0 - - + -
385B GLN* 4.6 4.0 - - - +
388B THR* 3.8 21.0 - - - +
390B GLU* 6.0 1.5 + - - -
561B SER* 3.3 12.7 + - - +
562B PHE* 3.4 25.0 - - - +
563B GLY 3.3 0.4 - - - -
564B ARG* 1.3 79.4 - - - +
566B LYS* 1.3 61.0 + - - +
568B LYS* 3.5 13.0 + - - +
569B LYS* 3.2 32.2 + - - +
611B ASP* 2.9 40.0 + - - -
613B GLU* 3.1 29.4 + - - +
614B ARG* 4.3 2.7 - - - +
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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
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562B PHE 3.5 10.7 + - - +
563B GLY* 3.2 10.9 + - - +
564B ARG 3.1 0.4 - - - -
565B ARG* 1.3 76.1 - - - +
567B LEU* 1.3 64.4 + - - +
568B LYS 3.1 2.0 - - - -
569B LYS* 2.9 32.6 + - + +
570B TRP* 3.1 43.3 + - + +
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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
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552B LEU* 4.2 14.8 - - + -
555B LEU* 3.7 31.6 - - + +
556B ASP* 3.8 24.0 - - - +
557B HIS 4.7 0.4 - - - +
558B THR* 4.3 11.2 - - + -
563B GLY 3.1 13.2 + - - +
564B ARG* 3.2 8.9 + - + +
566B LYS* 1.3 77.5 - - - +
568B LYS* 1.3 59.7 + - - +
570B TRP* 3.5 23.7 + - + +
571B VAL* 3.1 39.1 + - + +
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Residues in contact with LYS 568 (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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354B THR* 3.1 33.0 - - - +
355B SER* 5.4 3.4 - - - -
356B THR* 3.4 17.6 + - + +
358B TYR* 5.9 0.8 - - - -
411B SER 4.3 7.2 + - - -
412B LEU 4.0 5.3 + - - -
413B GLN* 2.8 35.2 + - - +
539B LEU* 4.2 18.4 - - + -
552B LEU* 4.0 29.1 - - + +
564B ARG* 3.1 11.7 + - + +
565B ARG* 3.6 13.5 - - - +
566B LYS 3.1 0.4 - - - -
567B LEU* 1.3 75.3 - - - +
569B LYS* 1.3 55.8 + - + +
571B VAL* 3.5 2.3 + - - +
572B THR* 2.8 36.4 + - + +
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Residues in contact with LYS 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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356B THR* 5.5 5.9 - - - +
358B TYR* 4.9 6.2 + - - -
385B GLN* 5.7 0.4 - - - +
390B GLU* 3.7 34.7 + - - -
565B ARG* 3.2 31.1 + - - +
566B LYS* 2.9 25.4 + - + +
568B LYS* 1.3 74.5 - - + +
570B TRP* 1.3 71.4 + - + +
572B THR* 3.0 18.5 + - - -
573B GLN* 3.0 32.7 + - - +
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Residues in contact with TRP 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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566B LYS* 3.1 44.2 + - + +
567B LEU* 3.8 26.0 - - + +
568B LYS 3.4 0.2 - - - -
569B LYS* 1.3 82.1 - - + +
571B VAL* 1.3 62.6 + - + +
573B GLN* 3.2 23.5 - - - +
574B PRO* 3.6 6.2 - - - +
584B ARG* 2.9 64.5 + - + +
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Residues in contact with VAL 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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528B ILE* 4.7 3.8 - - - +
538B ILE* 3.6 34.1 - - + +
539B LEU* 4.9 5.2 - - + -
551B LEU* 4.1 18.4 - - + -
552B LEU* 4.1 19.5 - - + +
555B LEU* 4.3 20.4 - - + -
567B LEU* 3.1 25.2 + - + +
568B LYS* 4.0 4.3 - - - +
569B LYS 3.1 0.8 - - - -
570B TRP* 1.3 74.3 - - + +
572B THR* 1.3 62.0 + - - +
573B GLN 3.1 6.0 + - - -
574B PRO* 3.7 13.7 - - - +
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Residues in contact with THR 572 (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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411B SER* 4.4 21.4 + - - +
526B MET 5.4 0.9 - - - +
528B ILE* 4.5 11.8 - - - +
533B LEU* 5.0 12.6 - - + +
538B ILE* 5.5 2.7 - - + -
539B LEU* 3.6 40.2 - - + -
568B LYS* 2.8 29.5 + - + +
569B LYS* 3.0 14.7 + - - -
571B VAL* 1.3 75.1 - - - +
573B GLN* 1.3 65.9 + - - +
574B PRO* 3.9 3.3 - - - +
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Residues in contact with GLN 573 (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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519B LEU* 4.1 14.5 + - - +
525B PHE* 3.7 50.8 - - + -
526B MET 5.2 2.2 - - - +
569B LYS* 3.0 32.3 + - - +
570B TRP* 3.2 11.8 - - - +
571B VAL 3.1 1.4 - - - -
572B THR* 1.3 87.3 + - - +
574B PRO* 1.3 68.9 - - - +
575B LEU* 4.1 10.9 - - - +
584B ARG* 5.5 0.2 + - - -
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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