Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 5X1A
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 GLY 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO 3.6 1.6 + - - -
68A GLY* 1.3 73.0 - - - +
70A ILE* 1.3 60.8 + - - +
100A GLY 2.9 15.1 + - - -
101A THR* 3.5 1.9 - - - +
102A THR* 2.9 22.8 + - - -
103A MET 3.2 6.8 + - - -
361A ARG* 3.6 5.6 - - - -
362A MET* 3.6 24.9 - - - -
384A THR* 3.5 11.2 - - - -
385A SER* 4.2 1.6 - - - -
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Residues in contact with ILE 70 (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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68A GLY 4.2 3.1 - - - +
69A GLY* 1.3 73.5 - - - +
71A ASP* 1.3 59.5 + - - +
72A VAL* 3.3 10.4 + - + +
103A MET* 3.3 26.5 - - + +
105A ILE* 4.2 28.7 - - + -
329A THR 3.8 3.3 - - - +
361A ARG* 3.4 9.4 + - - -
384A THR 2.8 19.6 + - - +
385A SER* 3.5 31.2 - - - +
388A ALA* 4.2 12.4 - - + +
389A ALA* 3.9 13.9 - - + +
394A LEU* 4.9 4.0 - - + -
398A LYS* 3.7 30.5 - - + -
399A GLY 4.3 0.4 - - - +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 1.3 69.9 - - - +
72A VAL* 1.3 56.7 + - - +
73A HIS 3.1 14.6 + - - +
74A THR* 3.5 13.2 - - + +
101A THR* 3.7 18.3 - - + +
103A MET 2.8 10.7 + - - +
104A ILE* 3.4 2.4 - - + +
105A ILE 2.8 26.6 + - - +
329A THR 4.4 0.2 - - - -
330A GLY* 3.1 1.9 - - - -
331A SER* 2.6 48.4 + - - -
358A THR* 2.9 17.2 + - - +
361A ARG* 3.5 17.9 + - - +
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Residues in contact with VAL 72 (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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70A ILE* 3.3 9.5 + - + +
71A ASP* 1.3 70.9 + - - +
73A HIS* 1.3 59.0 + - - +
105A ILE* 3.3 12.3 - - + +
107A HIS* 4.5 0.3 + - - -
138A HIS* 2.8 28.6 + - - -
251A TYR* 3.2 24.0 - - - +
277A GLU* 3.5 12.7 - - + +
328A VAL* 4.2 7.6 - - + -
329A THR 3.4 25.1 + - - +
330A GLY* 3.8 1.3 - - - -
388A ALA* 3.3 33.7 - - + -
392A PHE* 3.9 18.6 - - + -
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Residues in contact with HIS 73 (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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71A ASP* 3.1 16.5 + - - +
72A VAL* 1.3 82.0 - - - +
74A THR* 1.3 60.1 + - - +
75A ARG* 2.9 34.2 + - + -
105A ILE 3.5 2.0 - - - -
107A HIS* 3.3 26.6 + + - -
165A LEU* 6.2 0.2 - - + -
253A THR* 4.1 11.3 - - + -
254A LYS* 3.6 30.5 - - + -
277A GLU* 2.8 33.0 + - - +
330A GLY* 4.4 2.9 - - - -
331A SER* 3.3 2.6 + - - -
332A ALA* 2.7 47.6 + - + +
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Residues in contact with THR 74 (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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71A ASP* 3.5 25.1 - - + +
73A HIS* 1.3 78.0 - - - +
75A ARG* 1.3 71.8 + - - +
76A PHE* 3.6 31.2 - - + -
104A ILE* 3.4 29.3 - - + +
105A ILE 3.0 6.3 + - - -
106A ASP* 2.8 44.2 + - - +
107A HIS* 3.3 4.3 + - - -
331A SER* 4.0 3.8 - - - +
333A HIS 4.2 4.9 - - - +
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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