Contacts of the helix formed by residues 631 - 636 (chain A) in PDB entry 5I4A
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 TYR 631 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ASP* 3.2 20.1 + - + +
387A VAL* 3.3 35.8 - - + +
388A ARG* 3.4 61.3 + - + +
630A ASP* 1.3 100.5 - - + +
632A GLU* 1.3 66.7 + - - +
633A TRP* 3.1 5.8 - - - +
634A LYS* 3.0 30.0 + - + +
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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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379A TYR* 5.3 0.5 + - - -
381A GLY 5.5 1.6 - - - +
383A ILE* 3.7 26.5 + - + +
384A ASP* 2.9 15.3 + - - +
387A VAL* 4.5 3.4 - - - -
629A THR* 3.4 27.0 + - - +
631A TYR* 1.3 77.1 - - - +
633A TRP* 1.3 63.0 + - - +
635A LEU* 3.0 22.4 + - + +
636A TYR* 2.6 36.7 + - + +
1B U 3.9 18.1 - - - +
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Residues in contact with TRP 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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472A ILE* 4.5 4.3 - - + -
474A LYS* 4.6 3.2 - - + +
625A LYS* 3.6 26.7 - - + +
626A VAL* 3.6 48.3 + - + +
629A THR* 3.1 31.4 + - - +
630A ASP 3.6 18.9 + - - -
631A TYR 4.3 0.2 - - - -
632A GLU* 1.3 75.8 - - - +
634A LYS* 1.3 99.4 + - + +
635A LEU 3.1 0.2 - - - -
636A TYR* 3.0 14.1 + - - -
637A ILE* 3.0 46.2 + - + +
639A TYR* 4.3 28.3 - + + -
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Residues in contact with LYS 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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387A VAL* 3.8 21.8 - - + -
396A LEU 5.4 1.2 - - - +
422A PHE* 3.6 18.2 - - - -
630A ASP 5.5 1.8 + - - -
631A TYR* 3.0 29.6 + - + +
633A TRP* 1.3 116.9 - - + +
635A LEU* 1.3 61.4 + - - +
636A TYR 3.2 0.7 + - - -
637A ILE 3.8 6.3 - - - +
639A TYR 6.0 6.5 - - - -
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Residues in contact with LEU 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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383A ILE* 3.7 44.2 - - + -
387A VAL* 3.7 21.8 - - + -
396A LEU* 3.7 32.4 - - + +
398A PRO* 3.9 16.6 - - + -
418A LYS* 2.8 33.7 + - - +
422A PHE* 3.4 5.1 - - - -
632A GLU* 3.0 19.0 + - + +
634A LYS* 1.3 79.4 - - - +
636A TYR* 1.3 67.2 + - + +
1B U 4.5 17.5 - - + +
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Residues in contact with TYR 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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379A TYR* 5.1 0.3 + - - -
418A LYS* 5.0 0.7 - - - +
421A ASN* 5.5 2.1 + - - -
422A PHE* 3.7 9.6 - - - -
608A SER* 5.9 2.3 - - - -
614A TYR* 4.9 7.3 + - - -
618A TYR* 5.5 0.2 + - - -
621A HIS* 6.0 1.3 - - - +
625A LYS* 3.8 33.4 - - + +
632A GLU* 2.6 52.0 + - + +
633A TRP* 3.0 12.0 + - - +
635A LEU* 1.3 87.6 - - + +
637A ILE* 1.3 72.4 + - + +
638A PRO* 3.6 9.2 - - - +
1B U 3.2 40.2 - + - -
3B U 3.8 15.9 - - - -
4B A 5.3 7.9 - - - -
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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