Contacts of the helix formed by residues 677 - 684 (chain A) in PDB entry 1RY2
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 MET 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A SER 5.7 1.1 - - - +
322A GLY 4.6 6.3 - - - +
669A PRO* 2.8 37.8 + - - +
670A LYS 4.3 8.3 - - - +
671A THR* 3.7 33.7 - - + +
676A ILE* 1.3 72.4 - - - +
678A ARG* 1.3 63.8 + - - +
679A ARG* 3.3 22.9 - - + +
680A ILE* 3.3 48.8 + - + +
681A LEU* 3.7 2.8 + - - +
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Residues in contact with ARG 678 (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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444A GLU* 4.5 10.1 + - - +
445A PRO* 6.1 1.8 - - - +
573A GLY 5.5 3.8 + - - -
577A ASP* 3.9 27.7 + - - +
588A THR* 4.3 17.5 + - - -
592A GLU* 3.8 21.9 + - - -
605A ALA* 4.5 2.9 - - + +
606A VAL 3.5 17.9 - - - +
607A VAL* 3.4 21.0 - - + +
675A LYS* 5.8 1.4 - - - +
676A ILE* 3.0 66.6 + - + +
677A MET* 1.3 69.3 - - - +
679A ARG* 1.3 57.2 + - - +
680A ILE 2.9 5.4 - - - -
681A LEU* 2.9 15.9 + - + +
682A ARG* 2.8 32.9 + - - +
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Residues in contact with ARG 679 (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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322A GLY 3.2 23.4 + - - -
323A SER* 3.5 20.2 + - - +
324A THR* 3.6 35.7 - - - +
577A ASP* 4.2 5.7 + - - +
677A MET* 4.0 18.3 - - + +
678A ARG* 1.3 77.4 - - - +
680A ILE* 1.3 77.3 + - + +
682A ARG* 3.5 31.2 + - - +
683A LYS* 3.0 45.4 + - - +
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Residues in contact with ILE 680 (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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669A PRO* 3.9 19.5 - - + -
677A MET* 3.4 45.3 - - + +
678A ARG 2.9 0.4 - - - -
679A ARG* 1.3 109.6 - - + +
681A LEU* 1.3 55.6 + - + +
682A ARG 3.1 1.5 + - - -
683A LYS* 4.1 8.5 - - + +
684A ILE* 2.7 30.7 + - - +
686A ALA 2.9 32.4 - - - +
704A VAL* 6.1 2.0 - - + -
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Residues in contact with LEU 681 (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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605A ALA* 3.7 26.2 - - + -
607A VAL* 3.5 35.4 - - + +
608A GLY 3.8 4.9 - - - +
621A PHE* 4.2 33.5 - - + -
668A LEU* 4.9 4.0 - - + -
669A PRO* 4.0 11.7 - - + -
676A ILE* 5.0 2.7 - - + -
677A MET 3.8 10.1 - - - +
678A ARG* 2.9 12.5 + - + +
680A ILE* 1.3 78.3 - - + +
682A ARG* 1.3 60.5 + - - +
684A ILE 2.8 15.1 - - - +
685A LEU* 3.9 11.1 - - - +
686A ALA 4.6 3.4 - - - +
707A LEU* 4.0 27.4 - - + -
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Residues in contact with ARG 682 (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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576A ASP 3.2 24.7 + - - -
577A ASP* 3.6 20.8 + - - +
607A VAL* 3.9 15.9 - - + +
608A GLY* 3.1 23.8 - - - +
609A PHE* 3.1 17.6 - - - -
678A ARG 2.8 18.4 + - - +
679A ARG* 3.5 24.1 + - - +
681A LEU* 1.3 79.3 - - - +
683A LYS* 1.3 72.6 + - - +
684A ILE 2.5 6.8 + - - +
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Residues in contact with LYS 683 (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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324A THR* 5.8 1.8 + - - -
609A PHE* 3.2 14.0 - - - -
610A ASN* 4.5 6.6 + - - -
679A ARG* 3.0 34.1 + - - +
680A ILE* 4.1 10.3 - - + +
682A ARG* 1.3 80.6 - - - +
684A ILE* 1.3 75.2 + - + +
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Residues in contact with ILE 684 (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 PHE* 3.7 9.4 - - + -
680A ILE 2.7 14.8 + - - +
681A LEU 2.8 7.3 - - - +
682A ARG 2.5 7.0 + - - -
683A LYS* 1.3 97.8 - - + +
685A LEU* 1.3 68.9 + - + +
686A ALA 2.6 23.7 + - - +
708A ILE* 4.5 15.9 - - + -
712A LYS* 5.4 7.9 - - - +
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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