Contacts of the helix formed by residues 82 - 90 (chain D) in PDB entry 1XPU
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 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D TYR* 3.3 20.3 - - - -
81D VAL* 1.3 72.9 - - - +
83D PRO* 1.3 74.2 - - - +
84D SER* 3.0 10.9 + - - -
85D GLN* 2.8 49.6 + - - +
86D ILE* 3.2 13.0 + - - +
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Residues in contact with PRO 83 (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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61D GLY* 3.7 22.2 - - - +
62D PHE* 3.8 14.4 - - + -
80D TYR* 3.3 14.8 - - - +
81D VAL 3.8 0.4 - - - -
82D SER* 1.3 84.9 - - - +
84D SER* 1.3 52.8 + - - +
86D ILE* 3.4 16.6 - - + +
87D ARG* 2.8 39.9 + - + +
1J U 5.8 0.2 - - - +
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Residues in contact with SER 84 (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 SER* 3.0 10.2 + - - -
83D PRO* 1.3 77.9 - - - +
85D GLN* 1.3 64.9 + - - +
86D ILE 3.2 0.2 - - - -
87D ARG* 3.0 22.5 + - - +
88D ARG* 3.2 14.4 + - - +
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Residues in contact with GLN 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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80D TYR* 4.6 1.0 - - - +
81D VAL* 3.8 12.6 - - + -
82D SER* 2.8 43.4 + - - +
84D SER* 1.3 73.9 - - - +
86D ILE* 1.3 64.3 + - - +
87D ARG 3.3 0.7 + - - -
88D ARG* 3.5 12.8 + - - +
89D PHE* 3.0 32.6 - - + -
91D LEU* 3.7 3.8 - - + +
113D LEU* 2.8 52.2 + - - +
114D LEU* 4.6 4.9 - - - +
115D LYS* 5.4 0.2 - - - +
116D VAL* 4.3 16.9 - - + +
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Residues in contact with ILE 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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55D LEU* 4.7 0.7 - - + -
57D ILE* 4.0 20.0 - - + -
61D GLY 3.7 17.9 - - - +
63D GLY* 3.6 29.2 - - - +
81D VAL* 3.9 12.8 - - + +
82D SER 3.2 13.7 + - - +
83D PRO* 3.4 11.4 - - + +
85D GLN* 1.3 78.0 - - - +
87D ARG* 1.3 58.5 + - + +
90D ASN* 3.0 10.7 + - - -
91D LEU* 2.9 61.7 + - + +
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Residues in contact with ARG 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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83D PRO* 2.8 27.6 - - - +
84D SER* 3.0 14.3 + - - +
86D ILE* 1.3 79.3 - - + +
88D ARG* 1.3 64.7 + - - +
89D PHE 3.4 0.3 + - - -
90D ASN* 3.6 13.4 + - - +
25E ASN* 4.9 9.0 + - - +
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Residues in contact with ARG 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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84D SER 3.2 9.4 + - - +
85D GLN* 3.5 10.3 + - - +
87D ARG* 1.3 79.3 - - - +
89D PHE* 1.3 94.2 + - + +
125D GLU* 3.7 14.3 - - - +
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Residues in contact with PHE 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 GLN* 3.0 30.2 + - + -
88D ARG* 1.3 109.8 - - + +
90D ASN* 1.3 73.0 + - - +
91D LEU* 3.9 20.8 - - + +
116D VAL* 3.5 40.8 - - + -
119D VAL* 5.1 2.8 - - + +
124D PRO* 2.8 41.0 - - + +
125D GLU* 3.9 18.2 - - - +
126D ASN 5.2 11.6 + - - +
28E ARG* 5.1 1.4 - - - -
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Residues in contact with ASN 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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86D ILE 3.0 11.4 + - - +
87D ARG* 3.6 8.7 + - - +
88D ARG 3.6 0.2 - - - -
89D PHE* 1.3 83.5 - - - +
91D LEU* 1.3 51.5 + - - +
92D ARG* 5.2 2.2 - - - +
25E ASN* 3.8 45.0 + - - +
28E ARG* 2.6 67.6 + - + +
29E MET* 5.6 1.2 - - - +
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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