Contacts of the helix formed by residues 633 - 641 (chain A) in PDB entry 5UT1
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 633 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A PHE 4.5 0.3 - - - +
632A GLY* 1.3 77.2 - - - -
634A LEU* 1.3 65.0 + - - +
635A ASP* 2.5 25.1 + - - -
636A THR* 3.6 13.5 + - - -
637A TYR* 3.3 19.9 + - - +
677A LYS* 3.5 24.7 - - - +
679A ILE 3.1 7.9 - - - -
680A LEU* 4.3 2.7 - - - -
681A LEU 5.1 0.2 - - - -
905A 7DZ 4.3 22.1 + - - -
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Residues in contact with LEU 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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633A SER* 1.3 71.9 - - - +
635A ASP* 1.3 60.6 + - - +
637A TYR* 3.2 9.3 + - + -
638A LEU* 2.9 46.6 + - + +
649A TRP* 3.5 32.5 - - + -
653A VAL* 4.0 9.4 - - + -
676A ALA* 3.3 15.5 + - + +
679A ILE* 2.7 49.2 + - + +
680A LEU* 4.8 1.1 - - - +
681A LEU* 5.1 7.2 - - + +
695A ILE* 5.0 7.2 - - + -
746A ILE* 3.8 26.7 - - + -
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Residues in contact with ASP 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER* 2.5 33.1 + - - -
634A LEU* 1.3 74.4 - - - +
636A THR* 1.3 71.5 + - - -
638A LEU* 3.4 7.1 + - - +
639A LYS* 3.1 21.7 + - - +
676A ALA* 3.4 21.8 + - + +
677A LYS* 3.4 32.5 + - - +
745A GLU* 4.6 0.9 - - - +
750A GLY* 4.1 7.4 - - - +
752A LYS* 3.8 30.4 + - - +
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Residues in contact with THR 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A SER* 3.6 14.3 + - - -
634A LEU 3.4 0.2 - - - -
635A ASP* 1.3 88.2 + - - +
637A TYR* 1.3 64.6 + - - +
639A LYS* 3.1 7.7 + - + +
640A LYS* 2.9 28.5 + - + +
905A 7DZ 5.9 1.7 - - - -
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Residues in contact with TYR 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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631A PHE* 4.0 21.1 + + + +
633A SER 3.3 15.2 + - - +
634A LEU* 3.2 10.2 + - + +
636A THR* 1.3 79.9 - - - +
638A LEU* 1.3 58.5 + - - +
640A LYS* 4.8 1.3 - - - -
641A ASN* 2.9 66.1 + - + +
645A ILE* 4.1 12.1 - - + -
649A TRP* 3.7 38.0 + + - -
681A LEU* 3.4 28.0 - - + -
684A GLU* 2.5 40.3 + - + +
685A GLU 5.1 0.5 + - - -
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Residues in contact with LEU 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LEU* 2.9 42.1 + - + +
635A ASP* 3.8 7.2 - - - +
637A TYR* 1.3 77.8 - - - +
639A LYS* 1.3 62.9 + - - +
642A LYS* 3.1 27.9 + - - +
645A ILE* 4.1 14.8 - - + +
649A TRP* 3.9 25.1 - - + -
650A LYS* 5.7 0.2 - - - -
676A ALA* 4.5 5.2 - - + -
745A GLU 3.8 19.3 - - - +
746A ILE* 3.4 34.3 - - + +
749A GLY* 3.4 7.6 - - - +
750A GLY* 3.6 14.1 - - - +
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Residues in contact with LYS 639 (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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635A ASP 3.1 12.6 + - - +
636A THR* 3.1 11.0 + - + +
638A LEU* 1.3 79.0 - - - +
640A LYS* 1.3 61.7 + - - +
642A LYS* 3.3 21.1 - - - +
749A GLY 3.3 15.4 + - - +
750A GLY* 4.8 5.8 - - - +
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Residues in contact with LYS 640 (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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636A THR* 2.9 21.6 + - + +
637A TYR* 4.2 2.2 - - - +
639A LYS* 1.3 77.5 - - - +
641A ASN* 1.3 71.5 + - - +
642A LYS* 3.5 0.9 + - - +
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Residues in contact with ASN 641 (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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637A TYR* 2.9 71.3 + - + +
638A LEU 3.9 1.6 - - - -
640A LYS* 1.3 87.5 - - - +
642A LYS* 1.3 63.6 + - - +
643A ASN 3.2 3.4 - - - -
644A CYS* 3.0 33.8 + - - -
645A ILE* 3.3 16.5 - - + +
684A GLU* 5.0 2.4 + - - +
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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