Contacts of the helix formed by residues 572 - 583 (chain A) in PDB entry 6CNB
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 ASP 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A TYR* 1.3 78.3 - - - +
573A ARG* 1.3 83.5 + - - +
574A ALA 3.1 1.6 - - - +
575A THR* 2.8 15.3 + - - +
576A LEU* 2.3 39.5 + - - +
602A TYR 4.1 10.2 - - - +
603A LEU* 5.0 3.1 - - + -
604A TRP* 4.2 6.2 - - - -
16C THR* 5.1 9.2 - - + +
18C THR* 3.3 20.7 + - - -
20C PHE* 3.2 13.2 - - + -
23C PHE* 3.1 37.5 - - - +
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Residues in contact with ARG 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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572A ASP* 1.3 90.9 + - - +
574A ALA* 1.3 49.2 + - - +
576A LEU* 4.4 5.2 - - + -
577A THR* 2.2 52.3 + - - +
592A ILE* 3.6 37.9 - - + +
604A TRP* 3.0 52.9 - - + -
20C PHE* 3.9 12.3 - - + -
22C GLY* 4.0 17.7 - - - +
78H SER* 4.8 2.4 - - - -
79H TRP* 3.7 25.2 + - - -
81H PRO* 5.6 3.6 - - - +
81K MET* 4.0 3.3 - - - +
87K GLU* 2.4 46.1 + - - +
108K TYR* 5.3 0.2 - - - -
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Residues in contact with ALA 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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572A ASP* 3.1 0.8 - - - -
573A ARG* 1.3 77.3 - - - +
575A THR* 1.3 67.4 + - - +
577A THR* 3.5 1.0 - - - -
578A GLN* 2.9 19.8 + - - +
17C SER* 5.8 3.1 - - - +
20C PHE* 3.3 32.9 - - + -
77K ARG* 3.4 26.7 + - - +
81K MET* 3.5 19.1 - - + -
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Residues in contact with THR 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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571A TYR* 3.9 24.7 - - + -
572A ASP* 2.8 21.9 + - - +
574A ALA* 1.3 75.1 - - - +
576A LEU* 1.3 63.9 + - - +
578A GLN* 3.1 8.1 + - - +
579A LEU* 2.9 28.1 + - + +
704A PHE* 6.2 1.6 - - + -
1011B GLU* 6.1 0.4 - - - +
16C THR* 3.1 35.6 - - + +
77K ARG* 5.1 1.1 - - - +
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Residues in contact with LEU 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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571A TYR* 4.2 12.1 - - + -
572A ASP 2.3 34.9 + - - +
573A ARG* 4.4 4.5 - - + +
575A THR* 1.3 68.6 - - - +
577A THR* 1.3 72.7 + - - +
579A LEU* 2.9 8.4 + - - -
580A LEU* 2.8 42.6 + - + -
592A ILE* 4.8 17.9 - - + -
604A TRP* 3.4 39.0 - - + +
608A GLN* 5.4 0.2 - - + -
609A VAL* 3.8 33.9 - - + +
612A LEU* 5.2 5.4 - - + -
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Residues in contact with THR 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ARG* 2.2 39.5 + - - +
574A ALA 3.5 2.9 - - - -
576A LEU* 1.3 78.5 - - - +
578A GLN* 1.3 58.5 + - - +
581A SER* 2.9 24.4 + - - -
592A ILE* 5.4 2.3 - - - +
81K MET* 3.7 4.7 - - + -
87K GLU 3.7 11.6 + - - -
88K PHE* 3.1 37.1 - - + -
89K CYS 3.2 42.6 - - - +
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Residues in contact with GLN 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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574A ALA 2.9 13.9 + - - +
575A THR* 3.6 9.7 - - - +
577A THR* 1.3 76.5 - - - +
579A LEU* 1.3 59.8 + - - +
581A SER* 3.1 6.6 + - - -
582A MET* 2.8 47.4 + - + +
707A ASN* 4.8 11.0 - - - +
1008B ILE* 6.1 1.0 - - - +
1009B THR* 5.6 1.2 + - - -
74K ASN* 4.8 3.1 + - - +
77K ARG* 3.4 37.1 + - - +
90K GLY* 4.5 2.9 - - - -
91K TYR* 4.0 39.5 + - - +
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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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564A ILE* 5.3 4.7 - - + -
571A TYR* 3.7 38.8 - - + +
575A THR* 2.9 20.8 + - + +
576A LEU* 2.9 8.0 + - - +
578A GLN* 1.3 74.1 - - - +
580A LEU* 1.3 54.9 + - - +
581A SER 2.7 2.3 + - - -
582A MET* 2.7 39.5 + - - +
583A MET* 2.9 14.3 + - - +
609A VAL* 3.8 25.1 - - + -
700A LEU* 4.1 11.6 - - + +
704A PHE* 3.5 38.8 - - + -
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Residues in contact with LEU 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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576A LEU* 2.8 31.1 + - + +
579A LEU* 1.3 72.1 - - - +
581A SER* 1.3 59.9 + - - +
583A MET* 3.4 28.7 - - + +
590A PHE* 3.1 74.5 - - + -
592A ILE* 4.4 7.6 - - + -
609A VAL* 4.7 8.6 - - + +
612A LEU* 3.5 40.6 - - + -
88K PHE* 3.8 16.4 - - + -
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Residues in contact with SER 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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577A THR 2.9 13.8 + - - -
578A GLN 3.2 9.6 - - - -
579A LEU 2.7 3.6 + - - -
580A LEU* 1.3 72.2 - - - +
582A MET* 1.3 54.4 + - - -
583A MET 3.0 1.6 - - - -
584A SER 2.5 46.4 + - - +
585A ASP* 4.7 5.2 + - - -
586A GLY* 5.0 0.3 + - - -
590A PHE* 4.7 2.0 - - - -
88K PHE* 3.5 16.4 - - - -
90K GLY* 3.4 31.9 + - - -
91K TYR 3.7 8.2 + - - -
104K ARG* 4.6 4.2 - - - +
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Residues in contact with MET 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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578A GLN* 2.8 45.2 + - + +
579A LEU* 2.7 22.7 + - + +
581A SER* 1.3 71.8 - - - +
583A MET* 1.3 61.7 + - - +
584A SER* 3.1 5.5 + - - -
585A ASP* 4.2 2.9 + - - -
699A LYS* 3.1 23.6 - - - +
700A LEU* 4.7 3.8 - - + +
703A ARG* 3.4 52.4 - - + +
704A PHE* 3.5 13.0 - - + +
707A ASN* 5.0 10.1 - - + +
91K TYR 4.2 11.7 - - - +
92K SER* 4.3 13.1 + - - -
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Residues in contact with MET 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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579A LEU 2.9 12.9 + - - +
580A LEU* 3.4 35.4 - - + +
581A SER 2.8 2.6 + - - -
582A MET* 1.3 73.4 - - - +
584A SER* 1.3 57.4 + - - +
590A PHE* 3.8 18.6 - - + -
609A VAL* 4.4 8.5 - - - +
612A LEU 4.2 0.9 - - - +
613A LEU* 3.4 56.8 - - + +
616A PRO* 5.1 0.4 - - + -
696A ARG* 3.4 35.5 - - + +
699A LYS* 3.9 7.7 - - - +
700A LEU* 3.9 28.6 - - + +
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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