Contacts of the helix formed by residues 629 - 637 (chain A) in PDB entry 1XMI
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 THR 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A ALA 5.8 2.5 - - - -
614A ASP 4.2 17.7 - - - +
615A LYS* 4.6 10.3 - - - +
616A ILE* 3.9 4.7 - - - +
626A PHE* 3.3 8.1 - - - -
628A GLY* 1.3 77.0 - - - -
630A PHE* 1.3 63.5 + - - +
631A SER* 3.6 10.5 + - - -
632A GLU* 2.9 40.6 + - - +
633A LEU 3.1 17.3 + - - -
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Residues in contact with PHE 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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607A MET* 3.5 41.3 - - + -
610A LEU* 3.5 38.8 + - + +
611A LYS* 3.5 45.5 - - + +
613A ALA 5.6 1.8 + - - -
616A ILE* 3.8 13.7 - - + +
629A THR* 1.3 74.1 - - - +
631A SER* 1.3 63.3 + - - +
633A LEU* 3.3 22.7 + - + +
634A GLN* 2.8 55.4 + - + +
640A PHE* 5.3 3.6 - + - -
641A SER* 5.9 1.1 - - - -
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Residues in contact with SER 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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629A THR* 3.3 9.6 + - - -
630A PHE* 1.3 82.8 - - - +
632A GLU* 1.3 58.2 + - - +
634A GLN* 3.3 6.6 + - - +
635A ASN* 2.8 42.6 + - - +
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Residues in contact with GLU 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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626A PHE* 3.9 10.8 - - + -
627A TYR 5.0 0.2 - - - +
628A GLY* 3.6 8.8 - - - -
629A THR* 2.9 42.2 + - - +
630A PHE 3.3 0.2 - - - -
631A SER* 1.3 76.5 - - - +
633A LEU* 1.3 57.8 + - - +
635A ASN* 3.3 8.1 + - - +
636A LEU* 3.0 36.7 + - + +
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Residues in contact with LEU 633 (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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610A LEU* 4.9 0.2 - - + -
616A ILE* 3.8 7.0 - - + -
618A ILE* 4.0 5.8 - - + -
626A PHE* 3.4 50.3 - - + -
629A THR 3.1 4.6 + - - +
630A PHE* 3.6 34.3 - - + +
632A GLU* 1.3 78.4 - - - +
634A GLN* 1.3 57.6 + - + +
636A LEU* 4.1 2.0 - - - +
637A GLN* 2.8 37.6 + - - +
640A PHE* 3.4 57.7 - - + -
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Residues in contact with GLN 634 (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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607A MET* 3.7 15.0 - - - +
611A LYS* 5.3 3.0 + - - +
630A PHE* 2.8 45.1 + - + +
631A SER* 3.6 8.3 - - - +
633A LEU* 1.3 79.0 - - + +
635A ASN* 1.3 61.3 + - - +
637A GLN 3.9 6.5 - - - +
638A PRO* 3.2 33.6 + - - +
640A PHE* 6.1 1.6 - - + -
641A SER* 3.7 20.9 + - - +
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Residues in contact with ASN 635 (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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631A SER* 2.8 35.2 + - - +
632A GLU* 3.3 7.9 + - - +
634A GLN* 1.3 78.4 - - - +
636A LEU* 1.3 62.5 + - + +
638A PRO* 4.4 4.3 - - - +
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Residues in contact with LEU 636 (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 PHE* 3.8 26.0 - - + -
632A GLU* 3.0 23.5 + - + +
633A LEU* 4.1 2.5 - - - +
635A ASN* 1.3 78.5 - - + +
637A GLN* 1.3 61.2 + - + +
638A PRO* 3.5 7.3 - - - +
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Residues in contact with GLN 637 (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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625A TYR* 2.7 42.7 + - - -
633A LEU* 2.8 24.3 + - + +
634A GLN* 3.4 7.4 - - - +
636A LEU* 1.3 77.3 - - + +
638A PRO* 1.3 58.4 - - - +
639A ASP* 2.9 23.9 + - + +
640A PHE* 3.0 47.8 + - + +
641A SER 4.9 0.2 + - - -
643A LYS* 4.2 9.0 - - - +
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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