Contacts of the helix formed by residues 627 - 632 (chain A) in PDB entry 1XR2
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 ILE 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581A PHE* 4.5 3.1 - - + -
582A ARG* 3.9 29.8 - - + +
592A TRP* 4.1 14.4 - - + -
596A PHE* 4.1 12.6 - - + -
621A TYR* 3.7 34.8 - - + -
623A ASP 4.7 4.3 - - - +
624A PHE* 3.8 19.1 - - + +
626A GLU* 1.3 84.5 - - + +
628A ILE* 1.3 58.1 + - - +
629A GLU* 3.1 4.3 - - - -
630A TYR* 2.7 36.3 + - + -
631A ILE* 2.9 30.7 + - + -
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Residues in contact with ILE 628 (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 PHE* 2.7 27.2 + - + +
625A ASN* 4.1 12.3 - - - +
627A ILE* 1.3 71.8 - - - +
629A GLU* 1.3 71.9 + - + +
631A ILE* 3.3 9.0 + - + +
632A HIS* 3.0 24.6 + - - +
653A ALA* 4.0 17.3 - - + +
654A PHE* 3.7 39.3 - - + -
657A PHE* 3.5 30.7 - - + -
660A TRP* 3.7 17.0 - - + -
160B ASN* 5.3 4.3 - - + +
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Residues in contact with GLU 629 (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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626A GLU 6.2 0.2 - - - +
627A ILE 3.1 1.4 - - - -
628A ILE* 1.3 86.4 - - + +
630A TYR* 1.3 72.1 + - + +
632A HIS* 3.7 13.0 - - - +
633A GLN* 3.0 21.5 + - - +
657A PHE* 2.9 17.4 - - + -
159B ARG* 3.6 39.9 + - - +
160B ASN* 2.8 30.7 + - - +
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Residues in contact with TYR 630 (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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581A PHE* 4.0 6.2 - - + -
592A TRP* 4.0 17.2 - + + +
593A PRO* 4.4 9.6 - - + +
596A PHE* 3.6 66.6 - + + -
600A ILE* 3.9 9.1 - - + +
626A GLU 4.1 6.7 - - - -
627A ILE* 2.7 26.7 + - - +
629A GLU* 1.3 79.0 - - + +
631A ILE* 1.3 63.8 + - - +
632A HIS 3.1 1.3 - - - -
633A GLN* 3.0 34.9 + - - +
634A LEU* 3.8 6.8 + - - +
168B ASN* 2.8 36.5 + - - +
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Residues in contact with ILE 631 (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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581A PHE* 3.4 28.0 - - + -
619A MET* 3.7 26.0 - - + -
624A PHE* 4.1 12.6 - - + -
627A ILE* 2.9 31.8 + - + +
628A ILE* 3.6 13.9 - - + +
630A TYR* 1.3 75.9 - - - +
632A HIS* 1.3 58.6 + - - +
634A LEU* 3.0 29.9 + - + +
636A PHE* 3.6 15.5 - - + -
639A ILE* 4.0 20.2 - - + -
654A PHE* 5.0 1.3 - - + -
660A TRP* 4.1 17.9 - - + -
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Residues in contact with HIS 632 (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 ILE 3.0 16.4 + - - +
629A GLU* 3.7 8.3 - - - +
630A TYR 3.1 0.2 - - - -
631A ILE* 1.3 79.9 - - - +
633A GLN* 1.3 62.3 + - + +
634A LEU 3.3 5.3 + - - +
636A PHE* 5.8 0.4 - - - -
657A PHE* 3.4 42.7 - + + -
659A GLY 4.7 12.6 - - - -
660A TRP* 4.4 18.1 - + + -
661A ILE* 5.9 3.1 - - + -
662A LYS* 4.7 9.9 + - + +
1202A SO4 4.7 8.3 + - - -
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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