Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 1Q6X
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.9 14.8 - - + -
84A ASN* 2.8 29.4 + - - +
85A TRP* 1.3 93.5 - - + +
87A SER* 1.3 55.1 + - - +
88A GLU 3.4 2.0 - - - -
89A TYR* 3.1 10.7 + - + -
90A TRP* 2.7 48.6 + - + +
451A ILE* 5.2 4.0 - - + -
459A VAL 5.9 0.2 - - - +
514A ASN* 3.9 35.4 - - + +
517A LEU* 4.0 14.6 - - + -
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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
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84A ASN* 3.2 30.6 + - - +
86A VAL* 1.3 76.4 - - - +
88A GLU* 1.3 59.0 + - - +
90A TRP* 3.8 4.5 - - - +
91A LEU* 2.9 35.2 + - - +
456A GLU* 3.1 31.2 + - - +
458A ARG* 6.5 0.9 - - - -
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Residues in contact with GLU 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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78A ARG* 3.6 27.4 + - - +
84A ASN 5.1 0.2 + - - -
85A TRP 5.5 0.4 + - - -
86A VAL 3.4 0.6 - - - -
87A SER* 1.3 78.9 - - - +
89A TYR* 1.3 73.9 + - + +
91A LEU* 3.9 5.7 - - - +
92A ASN* 3.2 38.9 + - - +
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Residues in contact with TYR 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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78A ARG* 3.3 47.3 + - - +
85A TRP 3.7 13.5 - - - -
86A VAL* 3.1 7.9 + - + +
88A GLU* 1.3 88.2 - - + +
90A TRP* 1.3 58.0 + - - +
92A ASN* 4.0 4.3 - - - +
93A ASP* 3.0 31.7 + - - +
517A LEU* 4.0 18.7 - - + +
518A ALA* 3.8 34.8 - - + -
521A GLU* 3.7 32.2 + - + +
522A LEU* 3.5 23.6 + - + +
525A ASP* 6.1 0.9 - - - +
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Residues in contact with TRP 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 VAL* 2.7 34.1 + - + +
87A SER* 3.9 4.5 - - - +
89A TYR* 1.3 71.6 - - - +
91A LEU* 1.3 69.9 + - + +
93A ASP* 4.7 1.1 - - + -
94A MET* 2.9 66.1 + - + +
95A TYR* 3.6 29.2 - + - -
338A ASP* 4.2 4.0 - - - -
446A TYR* 5.0 1.4 + - - -
458A ARG* 3.6 53.8 - - + -
459A VAL* 3.6 36.6 + - + +
460A ASP* 5.8 0.2 - - - +
514A ASN* 3.6 20.6 - - - -
517A LEU* 3.9 12.1 - - + +
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Residues in contact with LEU 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 2.9 19.2 + - - +
88A GLU* 3.9 6.3 - - - +
90A TRP* 1.3 85.8 - - + +
92A ASN* 1.3 59.3 + - - +
95A TYR* 3.2 13.0 + - + +
96A LEU* 3.1 44.0 + - + +
182A LEU* 4.3 19.7 - - + -
335A SER* 3.5 38.1 - - - +
458A ARG* 4.7 7.0 - - - +
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Residues in contact with ASN 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 GLU* 3.2 31.9 + - - +
89A TYR* 4.1 3.9 - - - +
91A LEU* 1.3 76.1 - - - +
93A ASP* 1.3 65.0 + - - +
94A MET 3.6 0.3 + - - -
95A TYR 3.8 0.2 + - - -
96A LEU* 3.5 27.3 + - - +
97A ASN* 2.9 47.0 + - - +
179A GLN* 3.5 26.5 + - - +
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Residues in contact with ASP 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 TYR 3.0 18.9 + - - +
90A TRP* 4.1 1.5 - - + +
92A ASN* 1.3 78.4 - - - +
94A MET* 1.3 66.6 + - - +
97A ASN* 4.0 12.0 + - - +
98A ASN* 5.4 2.6 + - - +
517A LEU* 3.7 19.9 - - + +
520A ARG* 2.8 31.9 + - - +
521A GLU* 6.3 0.9 - - + -
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Residues in contact with MET 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 TRP* 2.9 44.7 + - + +
93A ASP* 1.3 84.4 - - - +
95A TYR* 1.3 104.5 + - + +
98A ASN* 4.4 13.0 + - - +
446A TYR* 4.5 30.5 - - + +
545A PHE* 6.5 1.8 - - + -
565A VAL* 5.3 13.0 - - + -
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Residues in contact with TYR 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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90A TRP* 3.6 33.5 - + - -
91A LEU* 3.2 10.3 + - + +
93A ASP 3.6 0.6 - - - -
94A MET* 1.3 112.4 - - + +
96A LEU* 1.3 67.3 + - + +
97A ASN 3.2 2.2 - - - -
98A ASN* 2.9 19.1 + - + +
106A SER* 3.9 21.5 - - - -
173A ARG* 2.8 29.5 + - - +
334A HIS* 2.8 58.7 + + + -
335A SER* 3.6 25.8 - - - -
458A ARG* 4.4 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