Contacts of the helix formed by residues 646 - 652 (chain A) in PDB entry 3RFU
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 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.0 8.7 - - - -
624A ASP* 5.3 0.2 - - - +
625A GLY* 3.2 32.6 + - - +
626A VAL* 4.4 8.3 - - + +
644A GLY* 2.5 29.8 + - - +
645A THR* 1.3 86.2 - - - +
647A VAL* 1.3 66.8 + - + +
648A ALA* 2.8 11.0 - - + +
649A ILE* 3.0 28.4 + - - +
650A GLU* 3.1 6.1 + - - +
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Residues in contact with VAL 647 (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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216A ILE* 4.7 0.3 - - - +
219A LEU* 3.3 30.5 - - + +
220A LEU* 3.4 36.8 - - + -
626A VAL* 3.6 39.3 - - + +
629A ALA* 3.5 26.9 - - + -
646A ASP* 1.3 76.6 - - + +
648A ALA* 1.3 53.5 + - - +
650A GLU* 3.3 2.7 + - - +
651A SER* 2.5 40.9 + - - +
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Residues in contact with ALA 648 (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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623A GLY 4.7 1.6 - - - +
624A ASP* 3.5 34.3 - - + +
625A GLY 3.5 18.8 - - - +
629A ALA* 5.0 1.1 - - + -
632A LEU* 4.4 13.1 - - + +
640A ALA* 3.2 11.3 - - + +
641A MET 6.0 0.2 - - - +
644A GLY 5.3 0.4 - - - +
646A ASP* 3.7 2.4 - - + +
647A VAL* 1.3 82.0 - - - +
649A ILE* 1.3 64.0 + - - +
650A GLU 3.1 0.2 - - - -
651A SER* 3.1 15.4 + - - -
652A ALA* 3.2 12.1 + - - +
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Residues in contact with ILE 649 (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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409A LYS* 4.1 11.0 - - - +
640A ALA* 3.5 8.2 - - + +
641A MET 4.1 10.5 + - - +
642A GLY* 4.1 17.0 - - - +
645A THR* 3.9 25.4 - - + +
646A ASP 3.0 31.0 + - - +
648A ALA* 1.3 78.6 - - - +
650A GLU* 1.3 76.5 + - + +
651A SER 3.7 0.3 + - - -
652A ALA 3.9 5.9 - - - +
655A THR* 3.4 42.6 - - + +
657A LEU* 6.4 0.2 - - + -
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Residues in contact with GLU 650 (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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215A ALA* 4.0 19.9 - - + +
216A ILE* 3.8 19.3 - - - +
219A LEU* 3.7 33.9 - - + -
326A GLN* 5.3 1.6 + - - -
409A LYS* 3.0 30.6 + - - +
646A ASP 3.1 5.7 + - - +
647A VAL 3.3 4.2 + - - +
648A ALA 3.1 0.8 - - - -
649A ILE* 1.3 95.5 - - + +
651A SER* 1.3 57.7 + - - +
652A ALA 3.5 2.5 - - - +
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Residues in contact with SER 651 (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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216A ILE* 3.1 25.2 - - - +
220A LEU* 5.0 0.2 - - - +
322A VAL* 4.9 1.2 - - - +
326A GLN* 6.1 0.4 - - - +
629A ALA* 4.0 17.0 + - - +
632A LEU* 3.8 19.9 - - - +
633A ALA* 4.0 21.2 + - - +
647A VAL* 2.5 27.2 + - - +
648A ALA* 3.1 6.6 + - - -
650A GLU* 1.3 75.5 - - - +
652A ALA* 1.3 60.5 + - - +
653A GLY 4.1 0.3 + - - -
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Residues in contact with ALA 652 (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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409A LYS* 3.8 13.2 - - - +
632A LEU* 3.9 6.1 - - + -
638A GLY* 3.0 35.4 - - - +
639A ILE 3.8 0.2 - - - +
640A ALA* 3.5 19.3 - - + +
648A ALA 3.2 5.8 + - - +
649A ILE 3.9 9.9 + - - +
650A GLU 3.5 2.1 - - - +
651A SER* 1.3 80.9 + - - +
653A GLY* 1.3 61.9 + - - +
654A VAL 3.3 13.1 + - - +
655A THR* 4.3 0.7 - - - +
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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