Contacts of the helix formed by residues 574 - 583 (chain A) in PDB entry 3C98
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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A PRO 4.4 2.0 - - - -
254A TYR* 4.0 42.3 + - + +
255A ASP* 5.0 1.1 - - - +
546A SER* 6.1 1.1 - - - -
547A LEU* 4.6 4.5 - - + -
572A ILE* 4.1 2.9 + - + +
573A LEU* 1.3 82.6 - - - +
575A PRO* 1.3 77.9 - - - +
576A GLN* 3.7 7.5 + - - +
577A LYS* 3.0 36.5 + - + +
578A LEU* 3.0 22.1 + - - +
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Residues in contact with PRO 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO 3.3 26.0 - - - +
243A VAL* 4.4 3.8 - - - +
244A LEU 4.2 7.6 - - - +
251A ALA 5.9 0.4 - - - +
255A ASP* 3.5 22.0 - - + +
406A ARG* 3.4 46.4 - - + +
546A SER* 6.4 1.8 - - - -
547A LEU* 6.4 0.7 - - + -
574A THR* 1.3 85.3 - - - +
576A GLN* 1.3 62.3 + - - +
578A LEU* 3.5 1.9 + - + +
579A LEU* 3.1 32.1 + - + +
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Residues in contact with GLN 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ASP* 5.1 11.4 + - - +
402A TYR* 4.2 23.8 - - + -
406A ARG* 5.1 1.9 - - - +
574A THR* 3.1 8.5 + - - +
575A PRO* 1.3 79.1 - - - +
577A LYS* 1.3 62.6 + - + +
579A LEU* 3.3 2.9 + - - +
580A ASP* 2.8 43.8 + - - +
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Residues in contact with LYS 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 6.0 3.2 - - - +
571A HIS* 4.9 13.5 - - - +
572A ILE 2.9 30.1 + - - +
573A LEU* 4.5 6.5 - - + +
574A THR* 3.0 29.5 + - + +
576A GLN* 1.3 77.8 - - + +
578A LEU* 1.3 65.3 + - - +
580A ASP* 3.4 10.4 + - - +
581A THR* 3.0 30.9 + - + +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 4.3 25.6 - - + -
235A ARG* 5.0 8.5 - - + -
239A PRO* 5.2 1.1 - - + +
242A PRO* 3.4 32.8 - - + +
243A VAL* 3.7 23.6 - - + -
443A MET* 4.6 11.2 - - + -
446A LEU* 5.8 1.1 - - + -
573A LEU* 4.0 23.9 - - + +
574A THR 3.0 11.7 + - - +
575A PRO* 3.7 8.3 - - + +
577A LYS* 1.3 76.7 - - - +
579A LEU* 1.3 63.2 + - + +
581A THR* 2.9 18.5 + - - -
582A LEU* 3.2 29.3 + - + +
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Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A VAL* 4.5 16.6 - - + -
402A TYR* 3.6 60.8 - - + +
405A ILE* 4.2 10.1 - - + -
406A ARG* 4.0 13.5 - - + -
409A LEU* 4.6 10.1 - - + -
439A ILE* 3.4 35.6 - - + +
575A PRO* 3.1 18.6 + - + +
576A GLN 3.6 2.7 - - - +
578A LEU* 1.3 88.9 - - + +
580A ASP* 1.3 64.4 + - - +
582A LEU* 3.4 3.4 + - + +
583A LYS* 3.2 16.5 + - - +
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Residues in contact with ASP 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 2.6 38.0 + - - -
576A GLN* 2.8 36.3 + - - +
577A LYS* 3.7 11.1 - - - +
578A LEU 3.3 0.2 - - - -
579A LEU* 1.3 76.7 - - - +
581A THR* 1.3 60.4 + - + +
583A LYS* 3.3 21.2 + - - +
584A LYS* 3.8 13.8 - - - +
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Residues in contact with THR 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 5.4 4.5 - - - +
153A PHE* 3.7 36.8 - - + -
154A GLN* 4.2 2.1 - - - +
571A HIS* 5.7 5.8 - - + +
573A LEU* 5.3 2.4 - - + +
577A LYS* 3.0 15.2 + - + +
578A LEU* 2.9 18.5 + - - -
580A ASP* 1.3 76.2 - - + +
582A LEU* 1.3 64.3 + - - +
583A LYS 3.1 1.8 - - - -
584A LYS* 3.2 29.0 + - - +
585A LEU* 3.6 14.6 + - - +
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Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 3.6 24.0 - - + -
409A LEU* 5.2 0.2 - - + -
439A ILE* 3.8 35.4 - - + +
442A ASN* 2.9 27.9 + - + +
443A MET* 3.5 39.9 - - + -
446A LEU* 3.8 21.1 - - + -
578A LEU* 3.2 24.7 + - + +
579A LEU* 3.8 8.7 - - + +
581A THR* 1.3 76.7 + - - +
583A LYS* 1.3 58.8 + - - +
584A LYS 3.0 1.4 + - - -
585A LEU* 3.3 14.8 + - + +
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Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 3.9 19.5 + - - +
435A GLU* 3.0 57.7 + - + +
436A ASP* 3.0 26.9 + - - +
438A GLU* 5.5 2.0 - - - +
439A ILE* 3.8 13.7 - - + +
442A ASN* 4.2 4.9 + - - +
579A LEU 3.2 10.5 + - - +
580A ASP* 3.3 17.0 - - - +
581A THR 3.1 0.2 - - - -
582A LEU* 1.3 77.7 - - - +
584A LYS* 1.3 58.7 + - + +
585A LEU 3.6 0.2 - - - -
586A ASN* 4.1 6.8 - - - +
587A LYS* 3.8 19.3 + - - +
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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