Contacts of the helix formed by residues 619 - 627 (chain C) in PDB entry 3UVJ
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 SER 619 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C LEU 2.9 22.1 + - - -
578C HIS* 2.8 35.7 + - - -
607C PHE* 3.6 20.5 - - - -
617C ASN 4.0 0.2 + - - -
618C VAL* 1.3 76.2 - - - +
620C PRO* 1.3 72.2 - - - +
621C THR* 3.1 10.6 + - - -
622C THR* 3.1 3.7 + - - -
623C TYR* 2.9 24.6 + - - +
646C PHE* 3.9 1.9 - - - -
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Residues in contact with PRO 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C SER* 1.3 88.9 - - - +
621C THR* 1.3 55.0 + - - +
623C TYR* 3.8 8.6 - - + +
624C ARG* 3.1 27.9 + - - +
642C LEU* 3.8 19.7 - - + -
646C PHE* 3.4 30.5 - - + -
650C ILE* 4.5 2.0 - - + -
651C PRO 3.6 22.2 - - - +
652C GLY* 4.0 7.2 - - - -
653C ILE 3.4 30.2 - - - +
655C HIS* 4.8 1.1 - - + -
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Residues in contact with THR 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C HIS* 3.3 7.9 + - + -
579C SER* 2.8 37.7 + - - +
619C SER* 3.1 14.3 + - - +
620C PRO* 1.3 76.4 - - - +
622C THR* 1.3 64.6 + - - +
624C ARG* 3.5 5.3 + - - +
625C LEU* 3.4 25.1 + - - +
646C PHE* 4.6 1.3 - - + -
650C ILE* 4.0 34.1 - - + -
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Residues in contact with THR 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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481C THR* 4.0 15.0 - - + -
546C ALA* 4.5 6.3 - - + +
577C LEU* 4.2 14.8 - - + -
578C HIS* 3.2 11.4 - - - -
579C SER* 2.8 37.1 + - - +
618C VAL* 3.7 16.4 - - + -
619C SER 3.1 7.0 + - - -
621C THR* 1.3 76.0 + - - +
623C TYR* 1.4 64.3 + - - +
625C LEU* 3.0 14.9 + - - +
626C LEU* 3.1 27.1 + - + +
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Residues in contact with TYR 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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618C VAL* 3.6 8.8 - - + +
619C SER 2.9 14.1 + - - +
620C PRO* 3.8 7.0 - - + +
622C THR* 1.4 76.1 - - - +
624C ARG* 1.4 55.9 + - + +
626C LEU* 3.1 4.5 + - - +
627C LYS* 2.8 67.2 + - + +
634C PHE* 3.8 37.9 - + + -
655C HIS* 3.2 53.6 - + + +
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Residues in contact with ARG 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C PRO 3.1 18.6 + - - +
621C THR* 3.9 6.7 - - - +
622C THR 3.3 0.4 - - - -
623C TYR* 1.4 79.1 - - + +
625C LEU* 1.3 63.3 + - + +
626C LEU 3.5 0.3 + - - -
627C LYS* 3.6 35.9 + - + +
628C ASP* 4.4 8.1 + - - +
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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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545C HIS* 3.7 27.4 - - + +
546C ALA* 3.7 15.9 - - + +
547C VAL* 5.2 1.0 - - - +
579C SER* 3.7 30.3 - - - +
621C THR 3.4 9.6 + - - +
622C THR 3.0 7.9 + - - +
624C ARG* 1.3 79.2 - - + +
626C LEU* 1.3 60.0 + - - +
628C ASP* 5.1 1.8 + - - +
629C CYS* 3.7 16.3 - - - -
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Residues in contact with LEU 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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546C ALA* 3.5 31.6 - - + +
547C VAL* 3.7 15.9 - - + +
550C ALA* 3.8 19.7 - - + -
577C LEU* 5.1 2.7 - - + -
618C VAL* 4.7 2.5 - - + -
622C THR* 3.1 33.6 + - + +
623C TYR 3.1 0.9 + - - +
625C LEU* 1.3 77.0 - - - +
627C LYS* 1.4 59.9 + - - +
628C ASP 3.2 3.4 - - - -
629C CYS* 3.0 31.6 + - - +
632C PHE* 3.8 22.0 - - + -
634C PHE* 3.7 35.9 - - + -
657C LEU* 5.2 0.4 - - + -
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Residues in contact with LYS 627 (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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623C TYR* 2.8 57.3 + - + +
624C ARG* 3.6 37.2 - - + +
625C LEU 3.8 0.2 - - - -
626C LEU* 1.4 72.6 - - - +
628C ASP* 1.4 76.3 + - - +
629C CYS 3.7 3.3 + - - +
634C PHE* 4.8 4.7 - - - -
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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