Contacts of the helix formed by residues 567 - 574 (chain A) in PDB entry 4BL8
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 567 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A ASN* 3.1 31.1 - - - +
425A PRO* 5.6 6.8 - - - +
564A ARG 5.0 0.9 - - - +
565A THR 3.4 11.0 - - - +
566A VAL* 1.3 84.6 - - + +
568A ILE* 1.3 68.0 + - + +
569A ALA 3.0 4.9 + - - -
570A GLY 3.3 10.9 + - - +
571A GLY* 3.4 19.6 + - - -
572A PRO* 5.9 1.1 - - + -
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Residues in contact with ILE 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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566A VAL* 3.1 5.1 + - + -
567A PRO* 1.3 85.8 - - + +
569A ALA* 1.3 57.3 + - - +
570A GLY 3.7 0.2 - - - -
575A ILE 5.7 0.2 - - - -
577A ASP* 4.1 18.1 - - - +
580A ARG* 3.2 22.8 - - + +
582A GLU* 5.0 6.3 - - + +
587A ILE* 3.6 37.2 - - + -
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Residues in contact with ALA 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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541A VAL* 5.0 3.8 - - - +
542A GLY 5.0 2.8 - - - +
563A LEU* 4.1 17.9 - - + +
566A VAL* 3.0 16.4 + - + +
568A ILE* 1.3 80.2 - - + +
570A GLY* 1.3 55.2 + - - +
575A ILE 3.9 8.3 - - - +
576A THR* 5.4 1.4 - - - -
577A ASP* 5.6 1.1 - - - -
580A ARG* 3.2 41.2 + - - +
584A ILE* 3.8 23.8 - - + -
587A ILE* 5.2 0.9 - - + -
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Residues in contact with GLY 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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425A PRO* 5.8 1.4 - - - +
563A LEU 3.8 4.5 - - - -
566A VAL 3.4 0.4 + - - -
567A PRO 3.3 7.4 + - - +
568A ILE 3.7 0.2 - - - -
569A ALA* 1.3 80.2 - - - +
571A GLY* 1.3 63.6 + - - +
572A PRO* 4.6 0.2 - - - +
573A TRP 3.8 2.1 + - - -
574A LEU* 2.9 16.2 + - - -
575A ILE* 2.9 46.2 + - - +
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Residues in contact with GLY 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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423A ASN 6.1 0.7 - - - -
563A LEU 3.2 7.9 + - - -
564A ARG* 3.2 32.5 - - - +
566A VAL 3.5 1.4 + - - -
567A PRO* 3.4 19.5 + - - -
570A GLY* 1.3 81.9 - - - +
572A PRO* 1.3 73.8 - - - +
574A LEU* 3.1 5.2 + - - -
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Residues in contact with PRO 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA* 4.9 9.6 - - + +
423A ASN* 5.4 4.7 - - - +
424A ILE* 4.4 22.7 - - + -
523A PRO* 4.6 5.5 - - - +
564A ARG* 3.8 31.8 + - + +
567A PRO* 5.6 0.9 - - + -
571A GLY* 1.3 84.0 - - - +
573A TRP* 1.3 73.9 + - + +
574A LEU* 3.4 0.9 - - - +
326B GLN* 4.3 28.1 + - + +
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Residues in contact with TRP 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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416A ASN* 3.8 23.1 - - - -
418A GLY* 4.8 7.9 - - - -
419A SER* 5.7 2.7 - - - -
424A ILE* 3.6 43.9 - - + +
427A HIS* 3.7 7.4 - + - -
463A ARG* 3.7 22.7 - - - -
523A PRO* 3.9 27.9 + - + +
524A GLN* 2.9 44.2 - - + +
539A GLN* 3.0 17.3 + - - +
570A GLY 3.8 0.8 + - - -
571A GLY 3.1 0.6 - - - -
572A PRO* 1.3 90.7 - - + +
574A LEU* 1.3 70.1 + - - +
575A ILE* 3.2 13.2 + - + -
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Residues in contact with LEU 574 (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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463A ARG* 4.7 0.3 - - - +
520A THR* 3.5 28.3 - - + -
521A GLU 5.8 0.2 - - - +
523A PRO* 6.3 2.0 - - + -
539A GLN* 2.7 27.8 + - - +
540A ILE 4.6 0.5 - - - +
541A VAL* 4.0 24.5 - - + +
560A LEU* 3.8 10.8 - - + +
563A LEU* 3.6 32.3 - - + +
564A ARG* 3.5 44.4 - - + +
570A GLY* 2.9 14.2 + - - -
571A GLY 3.1 6.8 + - - +
572A PRO 4.9 0.7 - - - +
573A TRP* 1.3 79.3 - - - +
575A ILE* 1.3 62.7 + - - +
576A THR* 3.7 2.8 + - - -
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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
------------------------------------------------------------
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