Contacts of the helix formed by residues 622 - 632 (chain A) in PDB entry 3RGZ
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 ARG 622 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A PHE* 3.4 37.5 - - + +
375A ASN* 3.4 14.6 + - - +
376A GLU* 5.2 4.0 + - - +
399A SER* 2.9 40.2 + - - +
400A ASN* 3.8 13.3 + - - +
401A ASN* 4.9 6.5 + - - +
425A ASN* 3.4 5.9 - - - +
618A PHE* 3.5 9.2 - - - -
621A ILE* 1.3 76.9 - - - +
623A SER* 1.3 65.4 + - - +
624A GLU* 3.6 26.7 - - - +
625A GLN* 2.9 55.5 + - - +
626A LEU 3.9 0.7 + - - -
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Residues in contact with SER 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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598A VAL* 5.8 0.9 - - - -
618A PHE* 3.6 20.1 - - - -
621A ILE 3.8 0.2 + - - -
622A ARG* 1.3 72.7 - - - +
624A GLU* 1.3 69.3 + - - +
626A LEU* 2.8 39.8 + - - +
627A ASN 4.6 0.2 + - - -
641A VAL* 5.4 7.0 - - - -
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Residues in contact with GLU 624 (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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622A ARG* 3.1 23.8 - - + +
623A SER* 1.3 95.4 + - - +
625A GLN* 1.3 64.7 + - - +
626A LEU 3.4 0.7 + - - -
627A ASN* 2.5 30.4 + - - +
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Residues in contact with GLN 625 (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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425A ASN* 3.0 35.7 + - - +
449A PHE* 3.6 12.4 - - + -
622A ARG* 2.9 51.8 + - - +
624A GLU* 1.3 85.6 + - - +
626A LEU* 1.3 58.2 + - - +
627A ASN* 3.0 9.4 - - - +
628A ARG* 2.9 50.8 + - - +
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Residues in contact with LEU 626 (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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449A PHE* 4.3 8.3 - - + -
472A TRP* 4.9 3.1 - - + -
598A VAL* 4.7 6.3 - - + -
600A ILE* 4.0 15.5 - - + -
618A PHE* 3.7 30.7 - - + -
622A ARG 3.9 0.8 + - - -
623A SER* 2.8 31.6 + - - +
625A GLN* 1.3 76.6 - - - +
627A ASN* 1.3 61.3 + - - +
628A ARG 3.0 0.7 - - - -
629A LEU* 3.0 47.2 + - + +
637A ILE* 4.1 17.5 - - + +
641A VAL* 4.0 35.2 - - + -
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Residues in contact with ASN 627 (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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624A GLU 2.5 31.0 + - - +
625A GLN* 3.0 14.8 - - - +
626A LEU* 1.3 76.7 - - - +
628A ARG* 1.3 70.8 + - - +
629A LEU 3.0 1.3 - - - -
630A SER* 3.0 26.6 + - - -
637A ILE* 3.5 25.0 - - + +
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Residues in contact with ARG 628 (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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425A ASN* 3.7 15.0 + - - -
426A ASN* 2.8 22.2 + - - +
449A PHE* 2.8 43.8 + - - +
450A ASN* 3.8 4.2 + - - +
451A TYR* 3.6 31.2 + - + +
473A LEU* 4.1 23.8 - - + +
625A GLN* 2.9 37.5 + - - +
627A ASN* 1.3 89.0 - - - +
629A LEU* 1.3 59.6 + - - +
630A SER* 3.2 2.2 + - - -
631A THR* 3.7 15.1 + - - +
632A ARG* 4.7 0.3 + - - +
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Residues in contact with LEU 629 (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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449A PHE* 4.9 1.6 - - + -
472A TRP* 4.4 5.6 - - + -
473A LEU* 4.1 22.7 - - + -
497A PHE* 4.0 38.6 - - + -
600A ILE* 4.2 15.3 - - + -
616A LEU* 4.6 11.7 - - + -
626A LEU* 3.0 40.4 + - + +
627A ASN 3.0 0.6 - - - -
628A ARG* 1.3 75.7 - - - +
630A SER* 1.3 64.2 + - - +
631A THR 3.1 2.9 - - - -
632A ARG* 2.9 16.2 + - - +
633A ASN* 2.9 31.9 + - + +
637A ILE* 5.4 3.6 - - + -
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Residues in contact with SER 630 (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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627A ASN 3.0 16.7 + - - -
628A ARG* 3.2 1.3 - - - -
629A LEU* 1.3 77.5 - - - +
631A THR* 1.3 64.7 + - - +
632A ARG 3.3 1.0 + - - -
633A ASN 3.7 10.1 - - - +
637A ILE* 3.8 21.4 - - - +
2D NAG 3.7 11.4 - - - -
3D NAG 2.8 26.9 + - - -
4D NAG 4.6 13.5 + - - -
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Residues in contact with THR 631 (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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628A ARG 3.7 12.8 + - - +
630A SER* 1.3 81.9 + - - +
632A ARG* 1.3 77.5 + - - +
1D NAG 4.7 0.3 + - - -
2D NAG 3.5 24.9 + - - +
3D NAG 3.3 27.1 - - - +
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Residues in contact with ARG 632 (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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450A ASN 5.8 0.8 + - - -
451A TYR* 6.2 1.2 - - - -
473A LEU* 3.8 24.5 - - + +
474A ASN* 2.9 25.0 + - - +
475A MET* 4.0 17.2 - - - +
497A PHE* 3.0 54.3 + - + +
498A ASN* 4.3 5.7 + - - +
499A ASP* 5.3 5.1 + - - -
521A ASN* 4.1 5.9 - - - +
628A ARG 4.7 0.7 - - - +
629A LEU* 2.9 9.3 + - - +
631A THR* 1.3 97.5 + - - +
633A ASN* 1.3 60.9 + - - +
1D NAG 3.4 41.4 + - - +
2D NAG 4.0 6.1 - - - -
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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