Contacts of the helix formed by residues 613 - 623 (chain A) in PDB entry 4N20
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 CYS 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A LEU* 3.8 11.5 - - + +
501A PHE* 4.2 13.7 - - - -
504A LYS* 4.4 27.8 - - + -
528A ILE* 4.9 0.2 - - - -
606A PRO* 2.9 47.7 + - - +
608A VAL* 4.2 17.3 - - + -
611A GLU 3.3 2.9 + - - -
612A CYS* 1.3 72.2 - - - +
614A LEU* 1.3 58.8 + - - +
616A MET* 4.0 7.6 - - - +
617A HIS* 3.0 29.1 + - - +
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Residues in contact with LEU 614 (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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497A CYS* 4.4 1.3 - - - -
500A LEU* 3.7 22.4 - - + -
501A PHE* 4.1 15.9 - - + -
570A PRO* 3.8 25.4 - - + -
585A PHE* 3.6 40.6 - - + -
588A MET* 4.1 5.2 - - + -
603A PRO* 3.7 15.9 - - + -
605A GLY* 3.6 25.1 - - - -
606A PRO* 4.4 4.3 - - + -
612A CYS* 3.2 8.1 - - - -
613A CYS* 1.3 76.4 - - - +
615A GLU* 1.3 59.7 + - - +
617A HIS* 3.3 1.8 + - - +
618A VAL* 2.9 35.5 + - - +
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Residues in contact with GLU 615 (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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602A LYS* 2.7 48.4 + - - +
603A PRO* 3.9 5.9 - - + +
611A GLU* 5.1 2.9 - - - +
612A CYS* 3.2 29.8 + - + +
614A LEU* 1.3 77.2 - - - +
616A MET* 1.3 77.4 + - + +
618A VAL* 3.3 0.9 + - - -
619A ARG* 2.9 30.5 + - - +
631A PHE* 3.6 45.0 - - + -
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Residues in contact with MET 616 (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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611A GLU* 3.7 43.5 - - + +
612A CYS 3.0 19.4 + - - +
613A CYS* 4.0 7.2 - - - +
615A GLU* 1.3 88.4 - - + +
617A HIS* 1.3 63.4 + - - +
619A ARG* 3.4 30.3 + - - +
620A GLY* 3.0 20.3 + - - -
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Residues in contact with HIS 617 (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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496A ALA* 5.0 10.5 + - + +
500A LEU* 3.9 33.0 - - + +
568A ASP 4.9 1.4 + - - -
570A PRO* 3.7 31.9 - - + +
613A CYS 3.0 19.1 + - - +
614A LEU* 3.7 4.0 - - - +
615A GLU 3.3 0.2 - - - -
616A MET* 1.3 77.3 - - - +
618A VAL* 1.3 61.6 + - - +
620A GLY* 3.1 3.6 + - - -
621A LEU* 3.1 46.1 + - + +
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Residues in contact with VAL 618 (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 LEU* 4.4 15.5 - - + -
570A PRO* 4.1 16.8 - - + -
588A MET* 3.7 28.9 - - + -
600A ILE* 4.0 19.3 - - + -
614A LEU 2.9 21.0 + - - +
615A GLU 3.9 2.5 - - - +
617A HIS* 1.3 73.1 - - - +
619A ARG* 1.3 65.7 + - - +
621A LEU* 3.1 9.2 + - - +
622A LEU* 3.0 43.4 + - + +
629A CYS* 4.7 0.9 - - - -
631A PHE* 4.2 11.2 - - + -
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Residues in contact with ARG 619 (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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615A GLU* 2.9 19.5 + - - +
616A MET* 3.7 30.7 - - - +
618A VAL* 1.3 75.6 - - - +
620A GLY* 1.3 58.6 + - - +
623A GLU* 2.8 74.4 + - - +
629A CYS* 3.0 39.9 + - + +
630A THR* 4.8 0.4 - - - +
631A PHE* 3.7 32.0 - - + +
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Residues in contact with GLY 620 (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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616A MET 3.0 15.3 + - - -
617A HIS* 3.1 5.1 + - - -
619A ARG* 1.3 76.7 - - - +
621A LEU* 1.3 60.3 + - - +
624A PRO* 3.3 21.2 - - - +
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Residues in contact with LEU 621 (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 ILE* 3.9 37.7 - - + +
568A ASP 3.3 26.9 - - - +
569A LEU* 3.9 12.8 - - + -
570A PRO* 4.6 0.7 - - + -
617A HIS* 3.1 44.0 + - + +
618A VAL* 3.1 7.8 + - - +
620A GLY* 1.3 80.8 - - - +
622A LEU* 1.3 63.2 + - + +
624A PRO* 3.9 5.8 - - - +
625A LEU* 3.9 8.1 - - - +
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Residues in contact with LEU 622 (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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488A LEU* 5.2 0.2 - - + -
490A LEU* 4.3 13.7 - - + -
567A ILE* 3.9 34.3 - - + -
569A LEU* 4.7 7.6 - - + -
591A MET* 4.8 5.8 - - + -
598A LEU* 3.8 23.3 - - + -
600A ILE* 4.2 4.5 - - + -
618A VAL* 3.0 32.7 + - + +
621A LEU* 1.3 79.3 - - + +
623A GLU* 1.3 65.5 + - - +
624A PRO 3.3 2.7 - - - -
625A LEU* 3.0 20.3 + - - +
627A LEU* 3.5 32.5 + - + +
629A CYS* 4.0 15.3 - - - -
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Residues in contact with GLU 623 (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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619A ARG* 2.8 75.0 + - + +
622A LEU* 1.3 71.8 - - - +
624A PRO* 1.3 63.9 - - + +
625A LEU 3.0 0.2 - - - -
626A GLY* 2.9 15.8 + - - -
627A LEU 3.5 17.9 - - - +
628A GLU* 5.3 0.6 - - - -
629A CYS* 4.5 8.1 + - - +
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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