Contacts of the helix formed by residues 62 - 69 (chain A) in PDB entry 2XAR
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 1.3 78.3 - - - +
63A SER* 1.3 66.1 + - - +
64A ASP* 3.4 9.5 + - - +
65A GLU* 3.0 50.1 + - - +
66A GLN* 3.1 12.2 + - - +
413A LEU* 4.9 1.0 - - - +
414A LYS* 6.0 7.6 - - + +
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Residues in contact with SER 63 (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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61A LEU 4.0 0.2 + - - -
62A THR* 1.3 74.3 - - - +
64A ASP* 1.3 65.5 + - - +
66A GLN* 3.7 14.8 + - - +
67A HIS* 3.6 16.6 + - - +
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Residues in contact with ASP 64 (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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62A THR* 3.1 7.4 + - - +
63A SER* 1.3 80.2 + - - +
65A GLU* 1.3 62.9 + - - +
67A HIS* 3.1 22.6 - - - +
68A LEU* 3.2 6.4 + - - +
325A ILE* 4.5 7.4 - - + +
326A ILE* 3.5 36.8 - - + +
413A LEU* 3.5 25.8 - - + +
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Residues in contact with GLU 65 (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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60A VAL 4.4 1.4 - - - +
61A LEU* 3.4 32.4 - - + +
62A THR* 3.0 48.9 + - + +
64A ASP* 1.3 74.8 - - - +
66A GLN* 1.3 59.5 + - - +
68A LEU* 3.3 1.7 + - - +
69A TRP* 3.0 45.2 + - + +
410A LEU* 5.2 3.6 - - - +
411A LYS 4.4 1.6 - - - +
412A PRO* 3.2 15.9 - - - +
413A LEU* 3.0 43.3 + - + -
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Residues in contact with GLN 66 (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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61A LEU* 4.2 22.1 - - + +
62A THR 3.1 13.4 + - - +
63A SER* 3.9 13.2 - - - +
65A GLU* 1.3 72.8 - - - +
67A HIS* 1.3 65.2 + - - +
70A ARG* 3.1 24.8 + - - +
76A ILE* 3.7 45.5 + - + +
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Residues in contact with HIS 67 (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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63A SER 3.6 7.4 + - - +
64A ASP* 3.1 20.8 + - - +
66A GLN* 1.3 80.6 - - - +
68A LEU* 1.3 55.3 + - - +
70A ARG* 3.2 55.0 + - - +
325A ILE* 5.2 10.9 + - + -
350A LEU* 4.0 17.4 - - + +
354A LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 68 (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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64A ASP 3.2 11.5 + - - +
65A GLU* 3.8 7.2 - - - +
66A GLN 3.2 0.2 - - - -
67A HIS* 1.3 76.3 - - - +
69A TRP* 1.3 77.9 + - + +
70A ARG* 3.0 9.0 + - - +
71A GLU* 4.5 4.5 + - - +
325A ILE* 4.7 6.1 - - + -
354A LEU* 3.5 48.3 - - + +
357A VAL* 4.2 10.5 - - + -
358A LYS* 3.9 32.9 + - + +
361A LEU* 3.7 30.3 - - + -
413A LEU* 4.4 14.8 - - + -
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Residues in contact with TRP 69 (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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61A LEU* 4.7 11.0 - - + -
65A GLU* 3.0 38.5 + - + +
68A LEU* 1.3 96.0 - - + +
70A ARG* 1.3 56.0 + - - +
71A GLU 3.2 2.9 - - - -
72A ASN* 2.9 46.7 + - - +
75A LEU* 3.7 22.2 - - + -
76A ILE* 3.5 14.9 - - + +
88A TYR* 3.6 25.4 - + - -
92A VAL* 4.2 16.4 - - + -
358A LYS* 3.7 29.6 - - + -
361A LEU* 4.6 14.7 - - + +
362A ILE* 4.0 10.8 - - + -
410A LEU* 3.3 32.6 - - + +
411A LYS 5.2 0.6 + - - -
413A LEU* 6.1 0.4 - - - +
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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