Contacts of the helix formed by residues 614 - 626 (chain C) in PDB entry 4Z2C
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 614 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612C VAL* 3.8 4.5 - - - +
613C ASP* 1.3 81.8 - - + +
615C ALA* 1.3 64.4 - - - +
616C ALA* 3.2 9.0 - - + +
617C GLU* 3.6 14.8 + - + +
618C ALA* 3.2 21.5 + - - +
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Residues in contact with ALA 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C TYR* 3.3 19.4 + - - +
527C LYS* 4.3 13.2 - - - +
612C VAL* 4.4 6.1 - - + +
613C ASP 4.4 0.2 + - - -
614C ASP* 1.3 70.7 - - - +
616C ALA* 1.3 61.4 + - - +
618C ALA* 3.8 2.2 - - - -
619C ASP* 2.9 29.1 + - - +
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Residues in contact with ALA 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C ASP* 3.2 6.0 - - + +
615C ALA* 1.3 75.4 - - - +
617C GLU* 1.3 61.2 + - - +
619C ASP* 3.3 5.8 + - - +
620C LYS* 2.9 30.2 + - - +
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Residues in contact with GLU 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 5.3 8.0 - - - -
613C ASP* 6.5 0.2 - - + -
614C ASP* 3.6 15.9 + - + +
615C ALA 3.5 0.2 - - - -
616C ALA* 1.3 78.1 - - - +
618C ALA* 1.3 56.5 + - - +
620C LYS* 3.7 6.9 - - - +
621C ILE* 2.9 30.1 + - - +
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Residues in contact with ALA 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.0 4.3 - - + -
12B THR* 5.2 9.1 - - - +
523C TYR* 3.6 26.9 - - + +
612C VAL* 4.1 11.0 - - + -
614C ASP 3.2 17.1 + - - +
615C ALA 3.6 0.9 - - - +
616C ALA 3.1 0.2 - - - -
617C GLU* 1.3 76.8 - - - +
619C ASP* 1.3 66.3 + - - +
621C ILE* 2.9 16.5 + - - +
622C PHE* 2.9 29.1 + - + -
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Residues in contact with ASP 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C GLU* 5.3 0.7 - - - +
523C TYR* 3.9 17.4 + - + +
615C ALA 2.9 21.6 + - - +
616C ALA* 3.8 4.5 - - - +
618C ALA* 1.3 72.7 - - - +
620C LYS* 1.3 58.1 + - - +
622C PHE* 3.5 4.8 + - - +
623C ASP* 2.9 29.3 + - - +
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Residues in contact with LYS 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C ALA 2.9 18.1 + - - +
617C GLU* 3.7 7.6 - - - +
619C ASP* 1.3 77.0 - - - +
621C ILE* 1.3 57.7 + - - +
623C ASP* 3.1 8.4 + - - +
624C MET* 2.9 34.2 + - + +
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Residues in contact with ILE 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 4.9 16.2 - - - +
15B MET* 5.8 4.9 - - + -
617C GLU 2.9 14.2 + - - +
618C ALA* 2.9 11.8 + - - +
620C LYS* 1.3 76.3 - - - +
622C PHE* 1.3 60.1 + - + +
624C MET* 3.2 7.8 + - - +
625C LEU* 2.9 46.9 + - + +
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Residues in contact with PHE 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.6 33.7 - - + -
12B THR* 6.1 1.1 - - - -
15B MET* 3.7 31.6 - - + -
463C GLU* 3.7 18.1 - - - +
519C LEU 3.7 4.3 - - - -
520C THR* 3.5 44.9 - - + -
523C TYR* 3.7 31.9 - + + -
524C ARG* 6.5 0.4 - - + -
618C ALA* 2.9 36.3 + - + +
619C ASP* 3.9 5.6 - - - +
621C ILE* 1.3 79.0 - - + +
623C ASP* 1.3 61.6 + - - +
626C MET* 3.1 31.0 + - - +
627C GLY 3.2 2.4 + - - -
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Residues in contact with ASP 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C GLU* 3.9 14.1 + - - +
619C ASP 2.9 18.6 + - - +
620C LYS* 3.4 9.0 - - - +
622C PHE* 1.3 77.5 - - - +
624C MET* 1.3 59.1 + - - +
627C GLY* 3.2 20.0 - - - -
629C ARG* 4.8 8.0 - - - +
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Residues in contact with MET 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C LYS* 2.9 17.9 + - + +
621C ILE* 3.6 6.7 - - - +
622C PHE 3.2 0.2 - - - -
623C ASP* 1.3 78.9 - - - +
625C LEU* 1.3 72.4 + - + +
626C MET 3.2 1.7 + - - -
629C ARG* 4.0 5.4 - - - +
632C PRO* 4.2 28.0 - - + +
633C ARG* 3.6 28.9 + - - +
636C PHE* 3.7 39.3 - - + -
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Residues in contact with LEU 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 4.1 28.9 - - + +
16B LYS* 4.3 7.6 - - + +
19B PHE* 3.5 52.7 - - + -
621C ILE* 2.9 30.4 + - + +
624C MET* 1.3 81.9 - - + +
626C MET* 1.3 77.5 + - + +
633C ARG* 2.9 22.1 + - + +
636C PHE* 3.6 32.3 - - + -
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Residues in contact with MET 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 4.4 3.4 - - + -
19B PHE* 4.5 6.5 - - + -
461C ASN* 2.8 55.3 + - - +
463C GLU* 3.4 15.0 - - + +
464C LYS* 4.2 4.3 + - - +
513C HIS* 5.6 4.3 - - + +
516C THR* 3.5 28.9 - - + -
517C LEU* 4.1 14.8 - - + -
520C THR* 3.5 27.1 - - + -
622C PHE* 3.1 21.6 + - + +
625C LEU* 1.3 95.9 - - + +
627C GLY* 1.3 68.7 + - - +
633C ARG* 3.8 3.0 + - - +
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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