Contacts of the helix formed by residues 85 - 95 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C PHE* 3.6 23.1 - - - -
83D ARG* 3.4 33.2 + - + +
84D HIS* 1.3 78.5 - - + +
86D SER* 1.3 61.4 + - - +
87D SER* 3.2 3.6 - - - -
88D LEU* 3.1 37.7 + - - +
89D GLN* 4.2 1.7 + - - +
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Residues in contact with SER 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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199C GLN* 4.1 17.5 + - - -
210C ASP* 3.8 12.1 + - - -
80D PHE 4.8 1.6 + - - -
81D TYR* 5.0 1.3 - - - -
82D GLY 4.8 6.4 + - - -
83D ARG* 3.7 35.5 - - - +
84D HIS 3.3 3.8 + - - -
85D ASP* 1.3 75.4 - - - +
87D SER* 1.3 63.4 + - - +
88D LEU 3.3 0.5 + - - -
89D GLN* 3.5 3.3 + - - +
90D LEU* 3.4 23.9 + - - +
195D GLY* 3.9 16.4 + - - +
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Residues in contact with SER 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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199C GLN* 3.5 16.8 + - - +
200C LEU* 4.2 12.9 - - - +
208C PHE* 4.0 27.5 - - - +
209C ASN 3.1 25.8 + - - -
210C ASP* 4.5 1.5 + - - -
212C ASN* 4.7 1.5 + - - -
85D ASP 3.1 0.4 + - - -
86D SER* 1.3 78.3 - - - +
88D LEU* 1.3 64.4 + - - +
90D LEU* 3.4 19.2 + - - +
91D THR* 3.4 17.3 + - - +
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Residues in contact with LEU 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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208C PHE* 4.3 29.7 - - + -
85D ASP* 3.1 35.7 + - - +
87D SER* 1.3 78.7 - - - +
89D GLN* 1.3 59.9 + - - +
91D THR* 2.6 27.1 + - - +
92D ARG* 3.4 47.0 + - + +
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Residues in contact with GLN 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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83D ARG* 5.8 2.7 - - - +
85D ASP 4.2 1.4 + - - +
86D SER* 3.5 4.0 + - - +
87D SER 3.3 0.2 - - - -
88D LEU* 1.3 76.4 - - - +
90D LEU* 1.3 62.0 + - - +
92D ARG* 3.1 17.5 + - - +
93D GLN* 2.8 27.7 + - - +
96D TRP* 3.9 6.5 - - - -
194D THR 3.4 27.1 - - - +
195D GLY* 3.6 20.4 - - - +
196D CYS* 3.7 15.3 - - - -
273D VAL* 3.6 17.8 - - - +
277D ASN* 3.1 41.2 + - - +
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Residues in contact with LEU 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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197C PHE* 4.5 9.4 - - + -
199C GLN* 4.0 41.3 - - + +
200C LEU* 4.3 12.1 - - + -
86D SER* 3.4 17.3 + - - +
87D SER* 3.4 9.8 + - - +
88D LEU 3.3 0.2 - - - -
89D GLN* 1.3 78.2 - - - +
91D THR* 1.3 63.4 + - - +
93D GLN* 3.1 9.8 + - + +
94D LEU* 2.9 34.4 + - + +
195D GLY 3.8 12.8 + - - +
197D PHE* 3.1 47.1 - - + -
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Residues in contact with THR 91 (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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200C LEU* 3.7 33.4 - - + -
208C PHE* 6.0 0.5 - - - -
87D SER 3.4 4.8 + - - +
88D LEU* 2.6 30.7 + - - +
90D LEU* 1.3 77.0 - - - +
92D ARG* 1.3 60.1 + - - +
94D LEU* 3.3 12.2 + - + +
95D ALA* 3.2 21.3 + - - +
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Residues in contact with ARG 92 (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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88D LEU* 3.7 49.9 + - + +
89D GLN* 3.1 24.9 + - - +
91D THR* 1.3 79.2 + - - +
93D GLN* 1.3 61.4 + - - +
95D ALA* 3.1 16.8 + - - +
96D TRP* 3.2 18.3 + - - -
277D ASN* 3.6 27.7 - - + +
279D GLU* 3.2 27.9 + - - +
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Residues in contact with GLN 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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89D GLN* 2.8 18.4 + - - +
90D LEU* 3.1 11.2 + - + +
92D ARG* 1.3 73.7 - - - +
94D LEU* 1.3 63.2 + - + +
96D TRP* 3.2 51.5 + - + +
195D GLY 4.4 1.4 - - - +
196D CYS* 3.1 14.4 - - - -
197D PHE* 2.8 51.8 + - - +
200D LEU* 3.7 26.9 - - + +
213D LEU* 3.7 13.1 - - - +
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Residues in contact with LEU 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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94C LEU* 3.6 41.3 - - + -
197C PHE* 5.3 1.6 - - + -
200C LEU* 4.2 23.1 - - + -
90D LEU* 2.9 26.6 + - + +
91D THR* 3.6 10.1 - - + +
92D ARG 3.2 0.2 - - - -
93D GLN* 1.3 78.6 - - + +
95D ALA* 1.3 58.9 + - - +
96D TRP 3.3 4.0 + - - +
197D PHE* 5.6 0.2 - - + -
200D LEU* 4.3 15.7 - - + -
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Residues in contact with ALA 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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91D THR 3.2 10.9 + - - +
92D ARG* 3.1 13.6 + - - +
93D GLN 3.1 0.6 - - - -
94D LEU* 1.3 77.2 - - - +
96D TRP* 1.3 64.5 + - - +
97D THR* 3.1 12.3 + - - +
278D GLN* 4.9 2.1 - - - +
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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