Contacts of the helix formed by residues 503 - 507 (chain A) in PDB entry 2XT6
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 GLN 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A LEU* 3.8 18.4 - - + +
497A GLN* 3.0 31.8 + - - +
500A TYR* 3.6 29.7 + - + +
501A VAL 4.1 6.5 + - - -
502A GLY* 1.3 85.8 + - - +
504A LYS* 1.4 62.6 + - - +
505A ARG 3.2 3.6 - - - -
506A PHE* 3.3 28.4 + - + +
507A SER 3.5 2.6 + - - -
561A PHE* 3.5 28.6 - - - -
575A ASP* 6.0 2.2 - - - +
578A TYR* 3.0 30.4 + - - -
749A GLU* 4.3 0.6 + - - -
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLN* 3.3 11.2 + - - +
502A GLY 3.5 1.2 - - - -
503A GLN* 1.4 77.2 - - - +
505A ARG* 1.4 61.5 + - - +
507A SER* 3.4 15.6 - - - -
540A ARG* 4.6 2.8 + - - -
745A ARG* 3.8 40.8 - - + +
746A GLY* 3.3 32.8 - - - +
747A HIS 4.2 1.3 - - - -
748A ASN 3.4 19.1 + - - +
749A GLU* 3.5 38.0 + - - +
750A GLY 4.9 3.2 - - - +
751A ASP 3.2 26.9 + - - +
753A PRO* 4.9 1.2 - - - +
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Residues in contact with ARG 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A GLY 4.4 6.4 + - - +
504A LYS* 1.4 78.6 - - - +
506A PHE* 1.3 99.4 + - + +
507A SER 3.4 0.7 - - - -
539A HIS* 3.5 32.5 + - + +
540A ARG* 3.4 21.1 + - - +
575A ASP 4.7 10.9 + - - +
579A HIS* 5.9 3.4 + - - -
604A SER* 5.5 5.7 + - - -
747A HIS* 3.2 26.4 + - + +
748A ASN* 4.5 13.8 - - + +
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Residues in contact with PHE 506 (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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493A GLU* 4.1 4.3 - - - +
496A LEU* 5.0 3.6 - - + +
497A GLN* 5.0 0.4 - - - -
502A GLY 3.4 21.1 - - - -
503A GLN* 3.3 38.5 + - - +
505A ARG* 1.3 113.1 - - + +
507A SER* 1.3 62.2 - - - +
508A LEU 3.4 1.6 + - - -
539A HIS* 3.2 32.5 - - + +
540A ARG* 4.3 8.1 - - - +
541A GLY* 3.1 21.1 + - - -
575A ASP 4.8 8.1 - - - -
578A TYR* 3.3 58.6 - + + +
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Residues in contact with SER 507 (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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493A GLU* 3.4 13.0 + - - -
497A GLN* 4.0 12.6 + - - +
503A GLN 3.5 2.4 + - - -
504A LYS 3.4 17.0 - - - -
505A ARG 3.4 2.6 - - - -
506A PHE* 1.3 76.0 - - - +
508A LEU* 1.3 56.0 + - - +
509A GLU* 3.2 27.2 + - - +
540A ARG* 2.9 31.6 + - - +
743A ARG* 5.1 2.7 - - - +
745A ARG* 3.4 24.4 + - - -
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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
------------------------------------------------------------
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