Contacts of the helix formed by residues 92 - 103 (chain D) in PDB entry 1XV2
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 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D SER* 1.3 73.0 - - - +
93D ASP* 1.3 66.5 + - - +
95D VAL* 3.1 3.6 + - - +
96D PHE* 2.8 53.8 + - + -
174D ILE* 5.0 0.7 - - - +
187D VAL* 4.2 6.1 - - - +
188D LEU 3.4 20.4 + - - +
189D ASP* 3.4 33.3 + - - +
190D PHE* 2.9 53.0 + - + +
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Residues in contact with ASP 93 (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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91D SER* 3.3 6.9 + - - +
92D GLN* 1.3 87.0 + - - +
94D ASP* 1.3 61.2 + - - +
96D PHE* 3.4 14.8 + - - +
97D ALA* 2.9 27.9 + - - +
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Residues in contact with ASP 94 (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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90D LEU* 4.1 28.8 - - + +
91D SER* 3.1 22.2 + - - +
93D ASP* 1.3 78.0 - - - +
95D VAL* 1.3 64.5 + - - +
97D ALA* 3.4 8.4 + - - +
98D GLN* 3.1 28.4 + - + +
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Residues in contact with VAL 95 (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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87D LEU* 4.1 21.8 - - + -
90D LEU* 3.7 24.5 - - + +
91D SER 2.9 16.8 + - - +
92D GLN 3.4 7.2 - - - +
94D ASP* 1.3 74.9 - - - +
96D PHE* 1.3 65.9 + - + +
98D GLN* 3.1 5.1 + - - +
99D ILE* 3.0 39.1 + - + +
114D ILE* 4.1 7.2 - - + -
190D PHE* 3.9 23.8 - - + -
192D VAL* 3.9 21.5 - - + -
197D VAL* 5.3 0.2 - - + -
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Residues in contact with PHE 96 (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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92D GLN* 2.8 49.8 + - + +
93D ASP* 3.7 14.1 - - - +
95D VAL* 1.3 81.6 - - + +
97D ALA* 1.3 57.4 + - - +
99D ILE* 3.3 11.6 + - + +
100D LYS* 2.9 39.1 + - - +
114D ILE* 5.4 2.5 - - + -
172D PHE* 3.5 47.4 - + + -
174D ILE* 3.6 30.3 - - + -
190D PHE* 4.0 17.9 - + - -
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Residues in contact with ALA 97 (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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93D ASP 2.9 17.4 + - - +
94D ASP* 3.6 11.4 - - - +
96D PHE* 1.3 78.7 - - - +
98D GLN* 1.3 63.7 + - + +
100D LYS* 3.4 16.1 + - - +
101D ASN* 3.0 27.4 + - - +
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Residues in contact with GLN 98 (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 PHE* 4.5 7.4 - - + -
87D LEU* 3.9 35.0 - - + +
90D LEU* 4.3 10.1 - - + -
94D ASP 3.1 18.7 + - - +
95D VAL 3.1 7.2 + - - +
97D ALA* 1.3 75.9 - - - +
99D ILE* 1.3 61.5 + - - +
101D ASN* 2.8 27.8 + - - +
102D GLU* 2.9 26.1 + - - +
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Residues in contact with ILE 99 (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 PHE* 4.4 4.5 - - + -
87D LEU* 5.3 0.4 - - + -
95D VAL* 3.0 27.0 + - + +
96D PHE* 3.7 13.7 - - + +
98D GLN* 1.3 76.1 - - + +
100D LYS* 1.3 57.0 + - - +
102D GLU* 3.0 1.2 + - - -
103D MSE 2.8 34.3 + - + +
110D SER* 5.7 1.6 - - - +
112D VAL* 3.9 17.0 - - + -
114D ILE* 3.9 27.8 - - + -
172D PHE* 3.5 31.6 - - + -
197D VAL* 4.2 20.9 - - + -
199D ILE* 3.7 20.9 - - + -
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Residues in contact with LYS 100 (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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96D PHE* 2.9 26.1 + - - +
97D ALA* 3.7 14.4 - - - +
99D ILE* 1.3 76.3 - - - +
101D ASN* 1.3 61.5 + - - +
103D MSE 3.3 45.3 - - + +
106D GLU* 5.1 7.9 - - - +
159D PHE* 4.3 14.8 - - + -
172D PHE* 3.9 17.3 - - + -
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Residues in contact with ASN 101 (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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97D ALA 3.0 15.3 + - - +
98D GLN* 2.8 21.6 + - - +
100D LYS* 1.3 79.8 - - - +
102D GLU* 1.3 69.3 + - - +
103D MSE 4.0 3.6 - - - +
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Residues in contact with GLU 102 (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 LYS* 3.0 54.3 + - - +
85D PHE* 3.4 49.3 - - + +
98D GLN* 2.9 22.4 + - + +
99D ILE 3.0 0.2 + - - -
101D ASN* 1.3 86.6 + - - +
103D MSE 1.3 66.4 + - - +
104D LEU* 3.8 0.3 + - - -
199D ILE* 3.8 7.7 - - + +
201D ASN* 5.5 1.0 + - - -
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Residues in contact with MSE 103 (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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99D ILE* 2.8 14.3 + - + +
100D LYS* 3.3 53.5 - - + +
101D ASN 4.0 5.9 - - - +
102D GLU* 1.3 81.7 - - - +
104D LEU* 1.3 65.3 + - - +
105D SER* 3.5 22.4 - - - +
106D GLU* 3.3 33.7 - - + +
110D SER* 4.4 10.5 - - - +
159D PHE* 4.0 22.9 - - + -
172D PHE* 5.5 1.8 - - - -
199D ILE* 3.9 15.8 - - + +
201D ASN* 3.8 11.7 - - - +
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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