Contacts of the helix formed by residues 85 - 95 (chain A) in PDB entry 5XVO
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 ASP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ARG* 2.9 28.3 + - - -
84A HIS* 1.3 106.0 + - + +
86A SER* 1.3 63.7 + - - +
87A SER 3.2 2.7 - - - -
88A LEU* 3.0 30.3 + - + +
89A GLN* 4.2 1.6 + - - +
207B GLN* 3.4 24.3 + - - +
208B PHE* 3.9 10.5 - - + -
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Residues in contact with SER 86 (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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81A TYR* 4.4 1.4 - - - -
82A GLY 4.8 5.8 - - - -
83A ARG* 3.5 32.3 + - - +
84A HIS 3.7 0.4 - - - -
85A ASP* 1.3 75.1 + - - +
87A SER* 1.3 63.4 + - - +
88A LEU 3.2 0.7 + - - -
89A GLN* 3.4 3.5 + - - +
90A LEU* 3.3 27.0 + - - +
195A GLY* 3.9 11.8 - - - +
199B GLN* 3.0 27.8 + - - +
210B ASP* 3.3 18.1 + - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP 3.1 0.6 + - - -
86A SER* 1.3 79.8 + - - +
88A LEU* 1.3 63.8 + - - +
90A LEU* 3.5 5.4 + - - +
91A THR* 3.4 25.4 + - - +
199B GLN* 3.5 32.2 + - - +
200B LEU* 5.3 2.5 - - - +
205B ALA 5.9 0.4 - - - -
206B ASN 3.8 10.4 + - - -
207B GLN* 3.6 17.4 + - - -
209B ASN 3.5 21.0 + - - -
210B ASP* 4.6 1.1 + - - -
212B ASN* 4.6 1.3 - - - -
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Residues in contact with LEU 88 (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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85A ASP* 3.0 24.5 + - - +
87A SER* 1.3 79.8 - - - +
89A GLN* 1.3 60.5 + - - +
91A THR* 2.6 26.5 + - - +
92A ARG* 3.4 39.9 + - + +
207B GLN* 4.1 38.0 + - + +
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Residues in contact with GLN 89 (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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83A ARG* 5.4 1.1 - - - -
85A ASP 4.2 1.2 + - - +
86A SER* 3.4 4.4 + - - +
88A LEU* 1.3 77.5 - - - +
90A LEU* 1.3 62.8 + - - +
92A ARG* 3.0 10.3 + - - +
93A GLN* 2.8 28.2 + - - +
96A TRP* 3.9 7.1 - - - -
194A THR* 3.4 27.1 - - - +
195A GLY* 3.5 20.6 - - - +
196A CYS* 3.7 14.5 - - - -
273A VAL* 3.6 18.2 - - - +
277A ASN* 3.1 42.0 + - - +
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Residues in contact with LEU 90 (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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86A SER* 3.3 16.2 - - - +
87A SER* 3.8 4.9 - - - +
88A LEU 3.3 0.4 - - - -
89A GLN* 1.3 76.6 - - - +
91A THR* 1.3 62.9 + - - +
93A GLN* 3.1 6.3 + - - +
94A LEU* 3.0 30.1 + - - +
195A GLY 3.0 23.3 - - - +
196A CYS 4.0 1.1 - - - +
197A PHE* 3.2 59.0 - - + +
199B GLN* 3.8 41.1 - - + +
200B LEU* 4.5 9.9 - - + -
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Residues in contact with THR 91 (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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87A SER* 3.4 12.2 + - - +
88A LEU* 2.6 30.8 + - - +
90A LEU* 1.3 73.7 - - - +
92A ARG* 1.3 59.5 + - - +
94A LEU* 3.3 13.5 + - + +
95A ALA* 3.3 21.3 + - - +
200B LEU* 4.7 15.5 - - + -
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Residues in contact with ARG 92 (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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88A LEU* 3.8 43.8 - - + +
89A GLN* 3.0 15.9 + - - +
91A THR* 1.3 78.3 + - - +
93A GLN* 1.3 63.5 + - - +
95A ALA* 3.1 16.9 + - - +
96A TRP* 3.2 18.3 + - - -
277A ASN* 3.6 33.2 + - - +
279A GLU* 3.5 31.6 + - - +
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Residues in contact with GLN 93 (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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89A GLN* 2.8 18.7 + - - +
90A LEU* 3.1 9.2 + - - +
92A ARG* 1.3 73.3 - - - +
94A LEU* 1.3 63.0 + - + +
96A TRP* 3.2 51.9 + - + +
196A CYS* 3.1 13.6 - - - -
197A PHE* 2.7 58.8 + - + +
200A LEU* 3.8 23.9 + - + +
213A LEU* 3.7 14.5 - - - +
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Residues in contact with LEU 94 (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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90A LEU 3.0 23.1 + - - +
91A THR* 3.6 12.8 - - + +
92A ARG 3.2 0.2 - - - -
93A GLN* 1.3 77.2 - - - +
95A ALA* 1.3 58.1 + - - +
96A TRP 3.3 5.0 + - - +
197A PHE* 4.6 6.5 - - + -
200A LEU* 4.2 13.9 - - + -
94B LEU* 3.5 44.4 - - + +
200B LEU* 4.8 16.4 - - + -
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Residues in contact with ALA 95 (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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91A THR 3.3 11.1 + - - +
92A ARG* 3.1 13.0 + - - +
93A GLN 3.1 0.8 - - - -
94A LEU* 1.3 76.5 - - - +
96A TRP* 1.3 65.3 + - - +
97A THR* 3.1 12.8 + - - +
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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