Contacts of the helix formed by residues 84 - 90 (chain D) in PDB entry 1XBT
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 VAL 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.7 0.6 - - + +
53D ILE* 3.7 36.1 - - + -
76D LEU* 4.3 23.8 - - + -
77D PRO 4.4 7.6 - - - +
78D ALA* 4.0 18.8 - - + -
81D LEU* 3.3 20.9 - - + +
82D ARG 3.1 0.2 - - - -
83D ASP* 1.3 83.7 - - + +
85D ALA* 1.3 65.0 + - - +
86D GLN 3.2 3.1 - - - -
87D GLU* 3.2 19.3 + - + +
88D ALA* 3.1 19.7 + - - +
108D PHE* 5.0 0.9 - - + -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU 3.2 7.3 + - - +
82D ARG* 3.3 24.2 + - + +
83D ASP 3.6 0.2 - - - -
84D VAL* 1.3 77.1 - - - +
86D GLN* 1.3 57.4 + - - +
88D ALA* 3.3 2.8 + - - +
89D LEU* 3.0 34.0 + - + +
108D PHE* 4.2 12.3 - - + -
112D MET* 4.0 15.7 - - + +
114G ASN* 6.4 0.2 - - - +
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ARG 5.0 0.4 + - - -
83D ASP 5.5 0.2 - - - -
84D VAL 3.2 0.8 - - - -
85D ALA* 1.3 75.5 - - - +
87D GLU* 1.3 75.6 + - + +
89D LEU* 3.4 23.3 + - + +
90D GLY* 3.8 3.8 + - - -
190E PHE* 3.1 60.8 + - + +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.0 9.6 - - + +
76D LEU* 4.0 30.2 - - + +
83D ASP 4.0 7.8 - - - +
84D VAL* 3.2 28.4 + - - +
86D GLN* 1.3 85.9 + - + +
88D ALA* 1.3 61.8 + - - +
89D LEU 3.3 0.7 + - - -
90D GLY* 3.3 13.2 + - - -
91D VAL* 4.0 10.0 + - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.7 17.0 - - + +
53D ILE* 5.0 0.4 - - + -
84D VAL 3.1 12.6 + - - +
85D ALA 3.3 8.7 + - - +
87D GLU* 1.3 76.0 - - - +
89D LEU* 1.3 61.2 + - - +
91D VAL* 3.4 19.1 + - - +
94D ILE* 3.7 28.7 - - + +
108D PHE* 3.8 20.2 - - + -
112D MET* 4.1 6.7 - - + -
117D LYS* 3.6 6.2 - - - -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 3.0 18.4 + - + +
86D GLN* 3.6 13.7 - - + +
87D GLU 3.2 0.4 - - - -
88D ALA* 1.3 77.2 - - - +
90D GLY* 1.3 55.8 + - - +
91D VAL 3.3 0.4 - - - -
112D MET* 3.7 32.5 - - + -
115D ALA* 5.3 8.1 - - + -
117D LYS* 3.0 27.2 + - - +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 3.6 25.3 + - - +
86D GLN 3.8 4.2 + - - -
87D GLU 3.3 8.2 + - - -
88D ALA 3.3 1.2 - - - -
89D LEU* 1.3 76.7 - - - +
91D VAL* 1.3 59.1 + - - +
117D LYS* 4.8 0.2 - - - -
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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