Contacts of the helix formed by residues 647 - 658 (chain A) in PDB entry 2RD0
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 ASN 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE* 6.0 0.2 - - - +
642A GLU* 3.0 37.3 + - + +
644A TYR* 3.1 12.1 - - + +
645A LEU 2.9 11.1 + - - +
646A ASP* 1.3 83.4 + - - +
648A LEU* 1.3 63.8 + - - +
649A LEU* 3.0 19.4 - - - +
650A VAL* 2.7 31.7 + - - +
651A ARG* 3.2 28.2 + - - +
683A ARG* 5.8 0.2 + - - -
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Residues in contact with LEU 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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609A PRO 4.3 8.7 - - - +
612A ARG* 5.7 1.6 - - + -
613A GLY* 3.3 34.1 - - - +
616A VAL* 4.0 18.7 - - + +
617A ARG* 5.1 7.2 - - - +
620A GLU* 5.9 2.2 - - - +
642A GLU* 5.5 0.9 - - - +
647A ASN* 1.3 75.4 - - - +
649A LEU* 1.3 65.7 + - - +
651A ARG* 3.2 13.1 + - + +
652A PHE* 3.1 20.6 + - - +
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Residues in contact with LEU 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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602A LEU* 4.1 21.1 - - + -
616A VAL* 3.7 16.7 - - + +
619A LEU* 4.8 1.3 - - + -
635A LEU* 4.2 15.9 - - + +
638A VAL* 3.3 34.8 - - + -
639A LEU* 4.5 9.6 - - + +
642A GLU* 3.1 26.1 + - - +
647A ASN* 3.0 7.8 - - - +
648A LEU* 1.3 70.8 - - - +
650A VAL* 1.3 65.1 + - - +
652A PHE* 3.1 20.3 + - + +
653A LEU* 3.0 38.7 + - + +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 4.7 14.4 - - + -
143A ILE* 5.3 2.7 - - + -
639A LEU* 3.6 20.0 - - + -
645A LEU 3.5 12.3 - - - +
647A ASN* 2.7 39.9 - - - +
649A LEU* 1.3 75.5 - - - +
651A ARG* 1.3 54.9 + - + +
653A LEU* 3.3 4.7 + - + +
654A LEU* 2.7 38.8 + - + +
687A LEU* 3.7 40.6 - - + -
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Residues in contact with ARG 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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142A ASN* 3.0 24.8 + - - +
143A ILE* 3.8 19.0 - - + +
145A ASN* 2.7 23.4 - - - +
146A VAL* 3.4 22.6 - - + +
646A ASP* 2.7 38.1 + - - -
647A ASN 3.2 19.2 + - - +
648A LEU* 3.2 14.1 + - + +
649A LEU 3.1 1.0 - - - -
650A VAL* 1.3 76.5 - - + +
652A PHE* 1.3 67.7 + - - +
654A LEU* 4.6 4.5 - - - +
655A LYS* 3.1 23.4 + - - +
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Residues in contact with PHE 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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616A VAL* 3.8 13.9 - - + -
619A LEU* 3.7 40.8 - - + -
620A GLU* 3.8 41.7 - - + +
623A LEU* 4.4 9.0 - - + -
628A LEU* 4.4 17.3 - - + -
635A LEU* 5.3 1.3 - - + -
648A LEU 3.1 12.5 + - - +
649A LEU* 3.1 24.7 + - + +
651A ARG* 1.3 74.9 - - - +
653A LEU* 1.3 74.2 + - + +
655A LYS* 3.0 15.0 + - - +
656A LYS* 3.1 45.3 + - + +
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Residues in contact with LEU 653 (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 LEU* 4.5 13.5 - - + -
632A LEU* 4.3 19.5 - - + -
635A LEU* 3.7 42.6 - - + +
636A VAL* 4.6 1.8 - - + +
639A LEU* 4.1 18.6 - - + -
649A LEU* 3.0 30.5 + - + +
650A VAL* 3.7 6.3 - - - +
652A PHE* 1.3 86.6 - - + +
654A LEU* 1.3 65.9 + - - +
655A LYS 2.9 0.7 + - - -
656A LYS* 3.1 6.6 + - - +
657A ALA* 2.9 25.5 + - - +
663A ILE* 5.5 1.2 - - + +
667A PHE* 4.1 16.2 - - + -
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Residues in contact with LEU 654 (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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143A ILE* 3.7 30.7 - - + -
146A VAL* 3.9 19.5 - - + -
147A CYS* 4.0 14.8 - - - -
650A VAL* 2.7 23.5 + - + +
651A ARG* 4.3 2.9 - - - +
653A LEU* 1.3 71.3 - - - +
655A LYS* 1.3 62.5 + - - +
657A ALA* 3.6 3.3 + - - +
658A LEU* 3.1 33.6 + - + +
667A PHE* 4.3 9.8 - - + -
687A LEU* 3.9 16.4 - - + -
690A SER* 3.8 18.4 - - - +
691A TYR* 3.8 30.1 - - + +
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Residues in contact with LYS 655 (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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146A VAL* 3.6 19.7 - - + +
149A GLU* 3.0 41.7 + - - +
150A ALA* 4.6 10.3 - - + +
153A LEU* 4.6 20.3 - - - +
651A ARG 3.1 17.7 + - - +
652A PHE* 3.0 7.5 + - - +
653A LEU 2.9 0.2 + - - -
654A LEU* 1.3 74.6 - - - +
656A LYS* 1.3 64.5 + - + +
658A LEU* 3.1 12.4 + - - +
659A THR* 2.8 27.1 + - - +
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Residues in contact with LYS 656 (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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619A LEU 5.9 0.2 + - - -
620A GLU 6.0 0.2 + - - -
623A LEU 4.5 11.7 + - - +
624A THR* 5.5 0.2 - - - +
625A ASP* 2.9 27.9 + - - +
628A LEU* 3.5 33.7 - - + -
652A PHE* 3.1 39.0 + - + +
653A LEU* 3.1 5.9 + - - +
655A LYS* 1.3 72.4 - - + +
657A ALA* 1.3 52.6 + - - +
658A LEU 2.7 4.6 + - - -
659A THR* 2.6 40.8 + - - -
660A ASN* 2.9 15.1 + - + +
663A ILE* 4.4 9.2 - - + -
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Residues in contact with ALA 657 (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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165A TYR* 4.4 4.3 + - - -
653A LEU 2.9 15.4 + - - +
654A LEU 3.7 4.7 - - - +
656A LYS* 1.3 76.4 - - - +
658A LEU* 1.3 58.0 + - - +
659A THR 3.7 0.2 + - - -
660A ASN 3.8 4.4 - - - +
663A ILE* 3.9 7.3 - - + +
664A GLY* 3.3 30.9 + - - +
667A PHE* 3.3 45.5 - - + -
691A TYR* 3.5 11.2 + - + -
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Residues in contact with LEU 658 (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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146A VAL 4.9 0.2 - - - +
147A CYS* 4.2 24.5 - - - +
150A ALA* 3.5 17.5 - - + +
154A ARG* 3.0 32.2 + - - +
165A TYR* 3.2 10.4 - - - -
654A LEU* 3.1 47.6 + - + +
655A LYS* 3.6 3.1 - - - +
656A LYS 2.7 3.0 + - - -
657A ALA* 1.3 75.2 - - - +
659A THR* 1.3 58.2 + - - +
691A TYR* 4.1 12.1 - - + +
694A ALA* 3.4 40.2 - - + +
695A CYS* 3.5 12.3 - - + +
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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