Contacts of the helix formed by residues 563 - 569 (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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A GLN* 2.8 24.7 + - - -
561A TYR 3.6 0.4 + - - -
562A ARG* 1.3 77.1 - - - +
564A ILE* 1.3 66.5 + - - +
565A GLU* 3.1 30.3 + - - -
566A VAL* 3.2 14.2 + - - +
567A LEU* 3.2 18.8 + - - +
576A ALA* 3.8 3.9 - - - +
579A TRP* 3.5 32.1 - - - -
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Residues in contact with ILE 564 (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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562A ARG 4.0 0.2 + - - -
563A SER* 1.3 72.8 - - - +
565A GLU* 1.3 68.3 + - - +
567A LEU* 3.1 10.2 + - + +
568A ILE* 3.1 31.6 + - + +
579A TRP* 3.9 31.8 - - + -
610A ILE* 4.1 20.4 - - + -
613A ILE* 3.9 21.1 - - + -
620A ILE* 4.0 25.8 - - + -
624A PHE* 4.2 14.4 - - + -
680A MET* 3.4 34.1 - - + +
685A ARG* 4.0 0.2 - - - +
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Residues in contact with GLU 565 (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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563A SER* 3.1 21.7 + - - +
564A ILE* 1.3 78.4 + - - +
566A VAL* 1.3 58.5 + - - +
568A ILE* 3.7 8.2 - - - +
569A GLY 3.1 6.1 + - - -
570A ALA* 2.8 32.4 + - + +
571A GLY 3.3 24.1 + - - +
572A TYR* 4.2 10.4 - - + +
573A SER 5.4 0.2 + - - -
575A PRO* 4.1 0.7 - - - +
576A ALA* 3.7 12.0 + - - +
624A PHE* 4.2 11.7 - - + -
682A PRO* 3.7 24.4 - - + +
685A ARG* 2.9 44.0 + - - -
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Residues in contact with VAL 566 (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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554A GLU 4.2 12.1 - - - +
555A ASP* 5.5 0.9 - - - +
556A ILE* 3.8 36.6 - - + +
557A GLN* 3.4 11.9 - - - +
562A ARG* 3.7 25.4 - - + -
563A SER* 3.2 24.8 + - - +
565A GLU* 1.3 76.9 - - - +
567A LEU* 1.3 62.5 + - - +
569A GLY* 3.1 13.4 + - - -
571A GLY 5.2 1.8 - - - +
572A TYR* 4.1 17.9 - - + -
630A TYR* 4.2 8.0 - - - -
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Residues in contact with LEU 567 (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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559A ARG* 3.5 15.9 - - - +
562A ARG* 3.7 23.3 - - + +
563A SER 3.2 16.7 + - - +
564A ILE* 3.1 9.1 + - + +
566A VAL* 1.3 79.9 - - - +
568A ILE* 1.3 60.3 + - - +
569A GLY 3.5 0.2 + - - -
606A ASP* 3.5 28.5 - - - +
609A HIS* 3.7 32.5 - - + +
610A ILE* 4.2 18.4 - - + -
613A ILE* 3.7 23.6 - - + -
630A TYR* 3.6 8.3 - - - -
634A PHE* 3.6 18.3 - - - -
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Residues in contact with ILE 568 (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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564A ILE* 3.1 30.4 + - + +
565A GLU* 3.7 8.3 - - - +
567A LEU* 1.3 77.4 - - - +
569A GLY* 1.3 57.1 + - - +
570A ALA* 3.9 16.2 - - + -
610A ILE* 4.2 15.5 - - + -
620A ILE* 5.8 0.9 - - + -
624A PHE* 3.3 42.2 - - + +
625A ALA* 3.9 11.0 - - - +
627A SER* 4.2 0.4 - - - +
628A GLY 3.3 6.2 - - - +
630A TYR* 2.7 34.6 + - - +
631A SER* 3.4 10.8 + - - +
634A PHE* 4.6 3.6 - - + -
635A PHE* 4.2 18.4 - - + -
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Residues in contact with GLY 569 (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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565A GLU 3.1 5.7 + - - -
566A VAL* 3.1 10.6 + - - -
567A LEU 3.2 0.2 - - - -
568A ILE* 1.3 80.6 - - - +
570A ALA* 1.3 58.3 + - - +
571A GLY 3.3 6.3 + - - -
628A GLY* 3.4 0.3 - - - -
629A LYS* 2.9 37.0 + - - +
630A TYR* 3.5 20.2 - - - -
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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