Contacts of the helix formed by residues 563 - 573 (chain A) in PDB entry 4ASQ
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 PRO 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.6 28.5 - - - +
209A GLU* 3.9 17.3 - - + +
562A LYS* 1.4 90.5 - - + +
564A TRP* 1.3 60.4 + - - +
565A PRO* 3.3 11.0 - - + -
566A ASP* 2.9 43.4 + - - +
567A ALA 3.6 1.4 + - - -
575A ARG* 6.3 0.7 - - - +
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Residues in contact with TRP 564 (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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207A GLU 5.2 0.4 - - - -
208A TYR* 2.7 34.0 + - - +
209A GLU* 4.8 6.7 + - + -
210A ASP* 4.3 16.2 - - - +
213A PHE* 3.9 20.0 - + - -
216A GLN* 4.9 3.8 - - - -
389A ALA* 3.7 27.8 + - + +
390A ASN* 3.2 31.0 - - + +
393A PHE* 3.6 25.0 - + + -
513A ILE* 5.9 2.5 - - + -
562A LYS 3.6 1.0 + - - -
563A PRO* 1.3 70.7 - - - +
565A PRO* 1.4 77.1 - - + +
566A ASP 3.1 0.2 - - - -
567A ALA* 3.0 4.5 + - - +
568A LEU* 2.9 35.0 + - + -
575A ARG 4.1 18.2 - - - -
576A ILE* 4.9 0.4 - - - -
577A MET* 3.8 36.3 - - + -
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Residues in contact with PRO 565 (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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209A GLU* 6.1 1.1 - - + +
210A ASP* 6.1 0.2 - - - +
563A PRO* 3.3 14.4 - - + +
564A TRP* 1.4 122.0 - - + +
566A ASP* 1.3 56.0 + - - +
568A LEU* 3.6 2.1 + - + -
569A GLU* 3.0 27.5 + - - +
574A GLU 3.6 5.7 - - - +
575A ARG* 3.5 48.4 + - + +
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Residues in contact with ASP 566 (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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558A MET* 3.8 8.1 - - + +
562A LYS* 3.7 29.2 - - + +
563A PRO* 2.9 35.1 + - - +
565A PRO* 1.3 74.9 - - - +
567A ALA* 1.3 60.8 + - - +
569A GLU* 3.5 7.5 + - - +
570A ALA* 3.1 26.0 + - - +
575A ARG* 2.6 35.9 + - - +
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Residues in contact with ALA 567 (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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374A TYR* 5.6 0.2 - - - +
389A ALA* 3.6 27.8 - - + -
393A PHE* 3.9 5.8 - - + -
555A MET* 3.2 30.6 - - + +
558A MET* 3.9 19.4 - - + +
559A GLY 5.2 3.1 - - - +
562A LYS 5.3 1.1 - - - +
563A PRO 3.6 2.9 + - - +
564A TRP* 3.0 10.6 + - - +
566A ASP* 1.3 77.1 - - - +
568A LEU* 1.3 64.2 + - - +
570A ALA* 3.3 9.4 + - - +
571A PHE 3.3 5.4 + - - -
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Residues in contact with LEU 568 (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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393A PHE* 4.0 13.1 - - + -
513A ILE* 6.0 3.6 - - + -
516A GLN* 4.1 16.6 - - + +
517A PHE* 3.6 27.4 - - + -
564A TRP* 2.9 23.9 + - + +
565A PRO* 3.8 4.0 - - + +
567A ALA* 1.3 75.6 - - - +
569A GLU* 1.3 62.8 + - - +
571A PHE* 3.0 14.1 + - - +
572A ASN* 3.1 37.9 + - - +
574A GLU* 3.3 18.8 - - + +
575A ARG 3.9 3.1 - - - -
576A ILE 3.6 36.1 - - - +
577A MET* 4.5 0.7 - - - +
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Residues in contact with GLU 569 (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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565A PRO 3.0 13.7 + - - +
566A ASP* 3.6 10.4 - - - +
567A ALA 3.3 0.2 - - - -
568A LEU* 1.3 75.7 - - - +
570A ALA* 1.3 60.2 - - - +
573A GLY* 2.8 44.2 + - - +
574A GLU 3.0 11.6 + - - +
575A ARG* 2.7 42.0 + - + -
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Residues in contact with ALA 570 (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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551A ALA* 4.5 0.5 - - - +
554A ASN* 3.7 37.2 + - + +
555A MET* 4.9 0.2 - - - -
558A MET* 3.6 26.9 - - - -
566A ASP 3.1 7.6 + - - +
567A ALA 3.5 10.1 - - - +
568A LEU 3.2 0.4 - - - -
569A GLU* 1.3 76.0 - - - +
571A PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 571 (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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517A PHE* 3.4 51.8 - + + -
520A SER* 3.8 11.7 - - - -
521A ALA* 4.1 7.9 - - + -
524A LYS* 3.3 25.4 + - - -
551A ALA* 3.4 34.0 - - + +
552A PHE* 3.7 46.7 - + - -
555A MET* 3.7 30.9 - - + +
567A ALA 3.3 1.8 + - - -
568A LEU* 3.0 10.8 + - - +
570A ALA* 1.3 81.8 - - - +
572A ASN* 1.3 70.4 + - + +
573A GLY 3.9 0.2 - - - -
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Residues in contact with ASN 572 (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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516A GLN* 4.0 10.9 + - - +
520A SER* 2.9 37.7 + - - +
524A LYS* 4.4 9.6 - - - +
568A LEU* 3.1 22.2 + - - +
571A PHE* 1.3 83.3 - - + +
573A GLY* 1.3 60.8 + - - +
574A GLU* 3.0 44.2 + - - +
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Residues in contact with GLY 573 (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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569A GLU* 2.8 35.1 + - - +
572A ASN* 1.3 77.8 + - - +
574A GLU* 1.3 61.4 + - - +
575A ARG* 4.8 1.9 - - - +
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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