Contacts of the helix formed by residues 651 - 661 (chain A) in PDB entry 2X7G
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 SER 651 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A LEU* 3.8 10.1 - - - -
650A TRP* 1.3 76.0 - - - +
652A LEU* 1.3 60.6 + - - +
653A PHE* 4.1 1.7 - - - +
654A ASP* 3.0 30.3 + - - -
655A VAL* 2.9 25.1 + - - +
1710A EDO 3.5 21.5 + - - -
1712A EDO 3.0 25.2 + - - -
1713A EDO 3.7 13.7 + - - -
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Residues in contact with LEU 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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586A PHE* 3.9 32.1 - - + -
594A LEU* 4.2 7.0 - - + -
616A LEU* 3.7 30.1 + - + +
651A SER* 1.3 72.8 - - - +
653A PHE* 1.3 63.1 + - - +
655A VAL* 3.3 4.9 + - + +
656A LEU* 3.1 31.8 + - + +
671A THR* 4.0 15.5 - - + +
674A LEU* 3.8 36.6 - - + -
675A ILE* 4.4 19.3 - - + -
678A LEU* 4.5 11.9 - - + -
1710A EDO 3.9 6.0 + - - +
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Residues in contact with PHE 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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651A SER* 3.3 3.3 - - - +
652A LEU* 1.3 78.1 - - - +
654A ASP* 1.3 80.5 + - - +
656A LEU* 3.4 3.1 + - - +
657A VAL* 3.0 44.7 + - + +
664A HIS* 3.5 41.1 - + + -
667A ALA* 4.0 7.2 - - + -
668A ALA* 3.7 28.0 - - + -
671A THR* 3.6 12.4 + - + +
1710A EDO 3.3 18.1 + - - +
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Residues in contact with ASP 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A TRP* 3.7 12.3 - - + -
651A SER* 3.0 16.4 + - - +
653A PHE* 1.3 91.5 - - - +
655A VAL* 1.3 57.8 + - - +
657A VAL* 4.5 3.2 - - - +
658A GLU* 2.8 62.4 + - - +
1712A EDO 2.4 24.9 + - - -
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Residues in contact with VAL 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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586A PHE* 3.9 12.1 - - + -
616A LEU* 4.4 4.3 - - + -
650A TRP* 3.6 41.0 - - + +
651A SER 2.9 18.0 + - - +
652A LEU* 3.3 9.4 + - + +
654A ASP* 1.3 74.4 - - - +
656A LEU* 1.3 58.6 + - - +
659A LYS* 2.8 41.2 + - + +
660A TYR* 3.5 22.5 + - + -
1711A EDO 3.7 30.5 - - - -
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Residues in contact with LEU 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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586A PHE* 4.1 23.6 - - + -
590A THR* 4.3 8.5 - - + -
652A LEU* 3.1 20.8 + - + +
653A PHE 3.8 5.4 - - - +
655A VAL* 1.3 78.4 - - - +
657A VAL* 1.3 61.1 + - - +
660A TYR* 3.4 11.9 + - + +
661A GLY 3.4 5.7 + - - -
662A TRP* 3.3 49.9 + - + +
667A ALA* 3.7 25.8 - - + +
670A PHE* 4.0 23.8 - - + -
671A THR* 3.7 24.2 - - - +
674A LEU* 5.6 0.4 - - + -
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Residues in contact with VAL 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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653A PHE* 3.0 40.3 + - + +
654A ASP* 4.2 3.4 - - - +
656A LEU* 1.3 76.1 - - - +
658A GLU* 1.3 69.7 + - + +
661A GLY* 3.0 24.8 + - - -
662A TRP 4.0 14.4 - - - +
664A HIS* 3.8 27.8 - - + +
667A ALA* 3.8 20.9 - - + -
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Residues in contact with GLU 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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650A TRP* 2.9 32.8 + - + +
654A ASP* 2.8 36.9 + - - +
657A VAL* 1.3 82.6 - - + +
659A LYS* 1.3 59.8 + - - +
661A GLY* 4.6 1.0 + - - -
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Residues in contact with LYS 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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592A ASP* 4.3 10.0 + - - +
593A TYR 5.9 0.4 + - - -
650A TRP* 4.0 27.7 - - + -
655A VAL* 2.8 27.3 + - + +
658A GLU* 1.3 75.0 - - - +
660A TYR* 1.3 97.1 + - + +
661A GLY 3.7 0.2 - - - -
1711A EDO 4.4 16.8 + - - -
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Residues in contact with TYR 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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586A PHE* 4.1 13.0 - + - -
590A THR* 3.8 36.1 - - + -
592A ASP* 2.6 37.6 + - - +
655A VAL* 3.7 24.9 - - + -
656A LEU* 3.4 17.6 + - + +
659A LYS* 1.3 116.7 + - + +
661A GLY* 1.3 62.3 + - - +
662A TRP* 3.2 21.0 + - + +
1711A EDO 5.3 0.5 + - - -
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Residues in contact with GLY 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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657A VAL* 3.0 18.5 + - - -
658A GLU 4.4 1.2 + - - -
659A LYS 3.7 1.2 - - - -
660A TYR* 1.3 76.2 - - - +
662A TRP* 1.3 65.3 + - - +
663A PRO* 3.6 3.6 - - - +
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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