Contacts of the helix formed by residues 570 - 581 (chain A) in PDB entry 6CIM
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 MET 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A ALA* 3.0 17.9 + - + +
567A LEU* 3.0 13.2 + - - +
569A ASP* 1.3 74.2 - - + +
571A GLU* 1.3 65.7 + - - +
572A GLU 3.3 3.1 - - - -
573A ASP* 3.0 17.8 + - + +
574A ILE* 2.9 27.0 + - + +
626A VAL* 3.8 35.2 - - + -
629A ILE* 4.0 15.7 - - - -
641A PHE* 3.5 24.9 - - + -
643A GLU* 5.4 0.2 - - - +
653A LYS* 6.5 0.9 - - + -
997A LYS* 3.5 34.1 - - + -
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Residues in contact with GLU 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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567A LEU 3.0 9.2 + - - +
568A MET* 3.2 28.3 + - - +
569A ASP 3.2 0.6 - - - +
570A MET* 1.3 75.2 - - - +
572A GLU* 1.3 70.4 + - + +
574A ILE* 3.2 3.2 + - - +
575A LEU* 3.0 37.9 + - + +
691A MET* 3.2 36.1 - - + +
692A GLY* 2.9 30.4 + - - -
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Residues in contact with GLU 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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569A ASP 4.4 4.4 + - - +
570A MET 3.3 1.0 - - - -
571A GLU* 1.3 87.1 - - + +
573A ASP* 1.3 63.0 + - - +
575A LEU* 3.4 7.2 + - + +
576A GLU* 2.9 30.7 + - - +
579A ARG* 4.9 1.7 + - - +
998A TYR* 4.2 26.5 + - + -
1001A LYS* 5.1 13.7 - - - +
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Residues in contact with ASP 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 ASP 4.8 1.0 - - - +
570A MET* 3.0 19.7 + - + +
572A GLU* 1.3 80.1 - - - +
574A ILE* 1.3 57.5 + - - +
576A GLU* 3.7 13.4 - - - +
577A GLY* 2.8 26.9 + - - -
640A VAL 4.3 2.6 - - - +
641A PHE* 4.3 27.1 - - + -
997A LYS* 4.4 21.9 + - - +
1001A LYS* 5.6 8.1 + - - +
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Residues in contact with ILE 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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567A LEU* 4.3 21.8 - - + +
570A MET* 2.9 23.1 + - + +
571A GLU 3.6 5.4 - - - +
573A ASP* 1.3 74.5 - - - +
575A LEU* 1.3 65.7 + - - +
577A GLY* 3.1 1.4 + - - -
578A MET* 2.9 28.6 + - + +
591A PHE* 4.3 27.4 - - + -
629A ILE* 3.6 31.9 - - + -
640A VAL* 4.4 13.6 - - + +
641A PHE* 4.9 6.7 - - + -
691A MET* 4.1 27.8 - - + -
698A PHE* 4.7 6.1 - - + -
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Residues in contact with LEU 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 GLU* 3.0 38.2 + - + +
572A GLU* 3.9 6.3 - - + +
574A ILE* 1.3 75.8 - - - +
576A GLU* 1.3 62.2 + - - +
577A GLY 3.3 0.2 + - - -
578A MET* 3.3 23.6 + - + +
579A ARG* 2.9 40.1 + - - +
585A ASP* 3.5 21.7 - - + +
691A MET* 4.2 15.7 - - + -
692A GLY* 5.2 8.1 - - - -
696A ARG* 3.8 23.3 - - - +
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Residues in contact with GLU 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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572A GLU 2.9 18.6 + - - +
573A ASP* 3.9 11.8 - - - +
575A LEU* 1.3 76.2 - - - +
577A GLY* 1.3 58.5 + - - +
579A ARG* 3.4 25.9 + - + +
580A SER* 2.9 32.0 + - - -
1001A LYS* 5.2 7.6 + - - -
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Residues in contact with GLY 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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573A ASP 2.8 14.1 + - - -
574A ILE 3.1 0.2 + - - -
576A GLU* 1.3 75.5 - - - +
578A MET* 1.3 63.8 + - - +
580A SER* 3.2 10.9 + - - -
581A GLN* 3.2 27.4 + - - +
640A VAL* 3.2 27.5 - - - +
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Residues in contact with MET 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 ILE* 2.9 15.5 + - + +
575A LEU* 3.6 39.9 - - + +
577A GLY* 1.3 74.0 - - - +
579A ARG* 1.3 63.2 + - - +
581A GLN* 3.2 6.7 + - - -
583A LEU* 2.8 44.5 + - + +
584A ASP 3.6 23.8 - - - +
585A ASP* 3.7 11.4 - - - +
587A LEU* 4.6 5.2 - - - +
591A PHE* 3.6 28.3 - - - -
631A ILE* 4.5 6.7 - - + -
640A VAL* 3.7 27.1 - - + +
696A ARG* 4.3 1.8 - - - +
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Residues in contact with ARG 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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572A GLU* 4.9 1.6 + - - +
575A LEU* 2.9 32.1 + - - +
576A GLU* 3.6 39.2 - - + +
578A MET* 1.3 76.1 - - - +
580A SER* 1.3 57.1 + - - +
582A ASP* 3.0 23.6 + - - +
583A LEU 3.8 11.0 - - - +
585A ASP* 2.8 41.9 + - - +
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Residues in contact with SER 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 GLU* 2.9 21.1 + - - -
577A GLY* 3.2 15.8 + - - -
578A MET 3.3 0.4 - - - -
579A ARG* 1.3 75.3 - - - +
581A GLN* 1.3 68.5 + - - +
582A ASP* 3.3 6.9 + - - +
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Residues in contact with GLN 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 GLY 3.2 18.5 + - - +
578A MET* 3.8 6.3 - - - +
579A ARG 3.1 1.0 - - - -
580A SER* 1.3 86.0 + - - +
582A ASP* 1.3 71.5 + - - +
583A LEU* 3.1 13.6 - - + +
638A VAL* 3.3 34.1 - - + +
639A LYS* 3.7 20.7 + - - +
640A VAL* 4.7 0.9 - - + -
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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