Contacts of the helix formed by residues 86 - 95 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.9 13.7 - - + -
84B ASN* 2.8 30.0 + - - +
85B TRP* 1.3 94.9 - - + +
87B SER* 1.3 55.0 + - - +
88B GLU 3.4 2.2 - - - -
89B TYR* 3.1 10.2 + - + -
90B TRP* 2.7 47.4 + - + +
451B ILE* 5.1 4.0 - - + -
459B VAL 5.9 0.2 - - - +
514B ASN* 3.9 36.8 - - + +
517B LEU* 4.0 15.0 - - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 3.2 31.6 + - - +
86B VAL* 1.3 76.8 - - - +
88B GLU* 1.3 59.1 + - - +
90B TRP* 3.9 4.5 - - - +
91B LEU* 2.8 35.4 + - - +
456B GLU* 3.1 32.5 + - - +
458B ARG* 6.5 0.7 - - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG* 3.6 27.4 + - - +
84B ASN 5.1 0.2 + - - -
85B TRP 5.6 0.2 - - - -
86B VAL 3.4 0.6 - - - -
87B SER* 1.3 78.5 - - - +
89B TYR* 1.3 74.3 + - + +
91B LEU* 3.5 5.9 + - - +
92B ASN* 3.2 39.3 + - - +
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 3.3 46.2 + - - +
85B TRP 3.7 13.5 - - - -
86B VAL* 3.1 7.6 + - + +
88B GLU* 1.3 87.4 - - + +
90B TRP* 1.3 59.2 + - - +
92B ASN* 4.0 4.8 - - - +
93B ASP* 3.0 31.7 + - - +
517B LEU* 4.0 18.5 - - + +
518B ALA* 3.8 35.0 - - + -
521B GLU* 3.7 31.9 + - + +
522B LEU* 3.5 23.4 + - + +
525B ASP* 6.0 0.7 - - - +
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Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 2.7 34.1 + - + +
87B SER* 3.9 4.9 - - - +
89B TYR* 1.3 71.7 - - - +
91B LEU* 1.3 70.4 + - + +
93B ASP* 4.7 0.7 - - + -
94B MET* 2.9 66.2 + - + +
95B TYR* 3.6 29.8 - + - -
338B ASP* 4.2 4.7 - - - -
446B TYR* 5.0 1.2 + - - -
458B ARG* 3.6 55.2 - - + -
459B VAL* 3.5 36.3 + - + +
460B ASP* 5.8 0.4 - - - +
514B ASN* 3.6 21.1 - - - -
517B LEU* 3.9 12.3 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B SER 2.8 23.0 + - - +
88B GLU* 3.9 5.6 - - - +
90B TRP* 1.3 83.0 - - + +
92B ASN* 1.3 58.2 + - - +
95B TYR* 3.2 14.0 + - + +
96B LEU* 3.2 42.1 + - + -
182B LEU* 4.3 20.0 - - + -
335B SER* 3.4 37.9 - - - +
458B ARG* 4.7 6.5 - - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 3.2 32.3 + - - +
89B TYR* 4.1 4.3 - - - +
91B LEU* 1.3 77.4 - - - +
93B ASP* 1.3 64.4 + - - +
96B LEU* 3.5 28.3 + - - +
97B ASN* 2.9 48.2 + - - +
179B GLN* 3.5 25.5 + - - +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR 3.0 18.7 + - - +
90B TRP* 4.1 1.7 - - + +
92B ASN* 1.3 77.8 - - - +
94B MET* 1.3 66.1 + - + +
97B ASN* 4.0 11.5 + - - +
98B ASN* 5.4 2.8 + - - +
517B LEU* 3.7 22.3 - - + +
520B ARG* 2.8 31.5 + - - +
521B GLU* 6.3 1.1 - - + -
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 2.9 44.9 + - + +
93B ASP* 1.3 84.0 - - - +
95B TYR* 1.3 103.0 + - + +
98B ASN* 4.4 13.4 + - - -
446B TYR* 4.5 31.2 - - + +
545B PHE* 6.5 1.6 - - + -
565B VAL* 5.3 13.2 - - + -
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 3.6 33.6 - + - -
91B LEU* 3.2 10.5 + - + +
93B ASP 3.6 0.4 - - - -
94B MET* 1.3 114.2 - - + +
96B LEU* 1.3 62.9 + - - +
97B ASN 3.2 2.5 - - - -
98B ASN* 2.9 24.5 + - - +
106B SER* 3.9 21.3 - - - -
173B ARG* 2.8 29.7 + - - +
334B HIS* 2.8 58.6 + + + -
335B SER* 3.6 25.6 - - - -
458B 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