Contacts of the helix formed by residues 611 - 621 (chain A) in PDB entry 4X8G
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 611 (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* 3.6 36.3 - - + +
501A PHE* 4.8 5.6 - - - -
504A GLN* 4.7 6.1 - - + +
526A ILE* 5.1 1.8 - - - -
604A PRO* 3.5 27.1 + - - -
606A ILE* 3.9 29.8 - - + -
609A ARG 3.4 3.7 + - - -
610A CYS* 1.3 70.5 - - - +
612A LEU* 1.3 73.8 + - - +
614A GLU* 3.3 9.8 + - - +
615A LYS* 3.1 18.4 + - - +
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Residues in contact with LEU 612 (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 6.1 - - - -
500A LEU* 3.7 20.2 - - + -
501A PHE* 3.9 20.4 - - + -
568A PRO* 4.2 22.9 - - + +
583A PHE* 3.8 26.7 - - + -
586A MET* 4.4 4.5 - - + -
601A PRO* 3.8 22.7 - - + -
603A GLY* 3.7 25.6 - - - -
604A PRO* 4.8 2.7 - - + -
610A CYS* 3.3 7.7 - - - -
611A CYS* 1.3 82.3 - - - +
613A GLU* 1.3 57.2 + - - +
615A LYS* 3.3 3.1 + - - +
616A VAL* 2.9 34.7 + - - +
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Residues in contact with GLU 613 (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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600A LYS* 2.8 44.6 + - - +
601A PRO* 3.6 22.6 - - + +
602A PHE* 4.8 1.4 + - - -
609A ARG* 6.4 0.4 - - + -
610A CYS* 3.4 26.8 + - + +
611A CYS 3.3 0.4 - - - -
612A LEU* 1.3 77.1 - - - +
614A GLU* 1.3 53.6 + - - +
616A VAL* 3.7 1.1 - - - +
617A CYS* 2.8 41.8 + - - -
629A PHE* 3.1 39.5 - - + -
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Residues in contact with GLU 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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609A ARG* 4.5 15.9 - - - +
610A CYS 3.1 14.1 + - - +
611A CYS* 3.4 14.1 - - - +
613A GLU* 1.3 78.0 - - - +
615A LYS* 1.3 56.8 + - - +
617A CYS* 4.0 7.1 - - - +
618A SER* 3.0 27.5 + - - -
621A GLU* 5.6 1.4 - - - +
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Residues in contact with LYS 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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496A SER* 2.6 48.5 + - - +
499A LYS* 4.6 9.9 - - - +
500A LEU* 4.3 33.3 - - + +
568A PRO* 4.4 12.6 - - + -
611A CYS 3.1 14.9 + - - +
612A LEU 3.9 3.6 - - - +
614A GLU* 1.3 73.7 - - - +
616A VAL* 1.3 66.9 + - - +
618A SER* 2.5 26.8 + - - +
619A LEU* 3.1 30.1 + - + +
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Residues in contact with VAL 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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567A ILE* 4.7 11.4 - - + -
568A PRO* 4.0 14.4 - - + -
586A MET* 3.7 31.9 - - + -
598A ILE* 4.8 10.8 - - + -
612A LEU 2.9 20.8 + - - +
613A GLU* 3.7 6.1 - - - +
615A LYS* 1.3 76.7 - - - +
617A CYS* 1.3 62.1 + - - +
619A LEU* 3.3 8.2 + - - +
620A LEU* 3.1 44.3 + - + +
627A CYS* 4.9 0.4 - - - -
629A PHE* 4.1 19.5 - - + -
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Residues in contact with CYS 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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613A GLU* 2.8 27.8 + - - +
614A GLU* 4.0 10.1 - - - +
616A VAL* 1.3 68.6 - - - +
618A SER* 1.3 57.6 + - - +
619A LEU 3.0 5.2 - - - -
621A GLU* 2.7 59.1 + - - +
627A CYS* 3.8 23.3 - - - -
629A PHE* 3.7 26.5 - - - -
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Residues in contact with SER 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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614A GLU* 3.0 17.4 + - - -
615A LYS* 2.5 30.2 + - - +
617A CYS* 1.3 75.6 - - - +
619A LEU* 1.3 65.4 + - - +
621A GLU* 4.6 4.9 - - - -
622A PRO* 3.3 21.2 - - - +
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Residues in contact with LEU 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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565A ILE* 4.2 27.2 - - + +
566A ASP 3.4 25.4 - - - +
567A ILE* 5.0 4.3 - - + -
568A PRO* 4.7 6.7 - - + -
615A LYS* 3.1 36.9 + - + +
616A VAL* 3.8 5.6 - - - +
617A CYS 3.0 0.6 - - - -
618A SER* 1.3 87.4 - - - +
620A LEU* 1.3 62.6 + - + +
622A PRO* 3.8 6.6 - - - +
623A LEU* 4.1 14.4 - - - +
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Residues in contact with LEU 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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479A VAL* 4.6 0.4 - - + -
490A LEU* 4.3 34.1 - - + -
565A ILE* 4.9 2.2 - - + -
567A ILE* 5.4 7.2 - - + -
589A MET* 5.0 2.5 - - + -
596A LEU* 3.6 24.5 - - + -
598A ILE* 4.7 5.6 - - + -
616A VAL* 3.1 37.0 + - + +
619A LEU* 1.3 83.6 - - + +
621A GLU* 1.3 64.2 + - - +
622A PRO 3.4 2.0 - - - -
623A LEU* 3.1 31.3 + - + +
625A LEU* 3.4 30.9 + - + +
627A CYS* 4.0 13.7 - - - -
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Residues in contact with GLU 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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614A GLU* 5.6 1.6 - - - +
617A CYS* 2.7 48.8 + - + +
618A SER* 4.4 2.9 + - - -
620A LEU* 1.3 72.6 - - - +
622A PRO* 1.4 59.2 - - + +
624A GLY* 2.8 22.7 + - - -
625A LEU 4.0 16.4 + - - +
627A CYS* 4.8 4.5 - - + +
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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