Contacts of the helix formed by residues 655 - 666 (chain A) in PDB entry 2R1Z
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 GLU 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A PRO* 1.3 82.4 - - + +
656A GLY* 1.3 67.7 + - - +
658A ARG* 3.3 8.4 + - - +
659A ARG* 2.7 70.2 + - - +
769A SER* 6.1 0.4 - - - -
771A GLU* 4.7 1.0 - - - +
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Residues in contact with GLY 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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624A ILE* 4.6 2.9 - - - -
655A GLU* 1.3 79.0 - - - +
657A PRO* 1.4 71.0 - - - +
659A ARG* 3.3 3.5 + - - +
660A SER* 3.0 21.1 + - - -
768A MET 3.6 15.0 + - - -
769A SER* 3.5 24.1 + - - +
770A PHE* 3.4 11.9 - - - +
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Residues in contact with PRO 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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614A VAL* 4.2 9.6 - - + -
624A ILE* 4.1 21.0 - - + -
628A CYS 4.5 4.0 - - - +
630A ILE* 3.6 36.8 - - + +
652A GLU* 4.1 3.4 - - + -
653A ILE* 3.6 28.9 - - + +
654A PRO 3.5 13.5 - - - +
656A GLY* 1.4 88.0 - - - +
658A ARG* 1.3 55.6 + - - +
660A SER* 3.4 3.5 + - - -
661A ARG* 3.0 30.0 + - - +
768A MET 4.3 6.7 - - - +
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Residues in contact with ARG 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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652A GLU* 3.4 31.1 + - - +
653A ILE 3.6 12.0 + - - +
654A PRO* 4.8 10.3 - - - -
655A GLU 3.3 12.4 + - - +
657A PRO* 1.3 74.4 - - - +
659A ARG* 1.3 69.0 + - - +
661A ARG* 3.3 7.2 + - - +
662A LEU* 2.9 54.8 + - + +
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Residues in contact with ARG 659 (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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655A GLU* 2.7 49.1 + - - +
656A GLY* 3.7 7.7 - - - +
658A ARG* 1.3 86.3 - - - +
660A SER* 1.3 57.6 + - - +
662A LEU* 3.8 8.3 - - + +
663A ASN* 2.9 27.4 + - - +
769A SER* 2.5 32.5 + - - +
770A PHE* 3.1 25.5 + - + +
771A GLU* 3.3 23.1 + - - +
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Residues in contact with SER 660 (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 ILE* 2.4 34.2 + - - -
627A GLY* 3.6 2.8 - - - -
656A GLY 3.0 14.7 + - - -
657A PRO* 3.7 4.3 - - - -
659A ARG* 1.3 72.8 - - - +
661A ARG* 1.3 61.0 + - - +
663A ASN* 3.2 0.7 - - - +
664A ARG* 2.9 24.4 + - - +
770A PHE* 3.4 25.0 - - - -
801A GOL 2.7 33.8 + - - -
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Residues in contact with ARG 661 (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 GLY* 3.9 23.6 - - - +
628A CYS 4.3 7.2 - - - +
629A TRP* 3.3 36.2 - - + -
649A GLU* 4.8 16.8 + - - +
652A GLU* 2.8 47.4 + - - +
657A PRO 3.0 17.2 + - - +
658A ARG* 3.5 15.7 - - - +
660A SER* 1.3 76.5 - - - +
662A LEU* 1.3 76.9 + - - +
664A ARG* 3.2 4.0 + - - +
665A GLU* 2.8 69.8 + - + +
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Residues in contact with LEU 662 (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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658A ARG* 2.9 61.6 + - + +
659A ARG* 3.8 9.0 - - + +
661A ARG* 1.3 103.8 - - - +
663A ASN* 1.3 56.9 + - - +
665A GLU* 3.8 10.8 - - + +
666A GLN* 3.0 55.2 + - - +
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Residues in contact with ASN 663 (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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659A ARG 2.9 16.3 + - - +
660A SER 3.2 9.6 - - - +
661A ARG 3.2 0.2 - - - -
662A LEU* 1.3 76.4 - - - +
664A ARG* 1.3 58.5 + - - +
666A GLN* 3.3 7.3 + - - -
667A LEU 3.2 3.8 + - - -
668A LEU* 3.0 54.5 + - - +
669A PRO 3.0 18.1 - - - +
722A TYR* 4.5 0.8 - - - -
723A HIS* 3.1 30.0 - - - -
770A PHE* 3.6 8.9 - - + -
801A GOL 3.2 23.4 + - - +
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Residues in contact with ARG 664 (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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604A VAL 5.8 1.6 + - - -
605A THR* 5.4 11.9 - - - +
626A ASN 3.2 25.3 + - - -
627A GLY* 3.5 17.4 + - - -
628A CYS* 6.0 1.2 - - - +
660A SER 2.9 11.7 + - - +
661A ARG* 3.2 7.8 + - - +
663A ASN* 1.3 75.2 - - - +
665A GLU* 1.3 62.5 + - + +
667A LEU* 2.9 27.8 + - - +
801A GOL 3.4 29.6 + - - +
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Residues in contact with GLU 665 (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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629A TRP* 4.3 9.5 - - - -
661A ARG* 2.8 62.3 + - + +
662A LEU* 3.8 12.4 - - + +
664A ARG* 1.3 77.9 - - + +
666A GLN* 1.3 60.9 + - + +
667A LEU* 3.3 11.4 + - - +
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Residues in contact with GLN 666 (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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662A LEU* 3.0 45.8 + - - +
663A ASN* 3.9 4.5 - - - +
664A ARG 3.1 0.4 - - - -
665A GLU* 1.3 77.8 - - + +
667A LEU* 1.3 71.8 + - - +
668A LEU* 3.2 32.6 + - + +
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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