Contacts of the helix formed by residues 85 - 98 (chain C) in PDB entry 3QN3
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 ASN 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B ARG* 4.6 4.2 + - - +
405B GLU* 4.4 20.3 + - - +
82C ASP* 3.4 32.2 + - - +
83C ALA 4.8 1.3 - - - -
84C PHE* 1.3 75.0 - - - +
86C GLN* 1.3 66.0 + - - +
87C THR* 3.6 8.5 + - - +
88C GLN* 3.0 47.8 + - + +
89C LEU* 3.0 21.4 + - - +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 4.9 2.1 - - - +
136B ALA* 4.5 20.9 - - + +
83C ALA 4.9 1.9 + - - +
84C PHE 3.3 6.7 + - - +
85C ASN* 1.3 74.6 + - - +
87C THR* 1.3 58.1 + - - +
89C LEU* 3.1 12.0 + - - +
90C ASP* 2.9 55.0 + - - +
114C SER* 3.0 32.0 + - - +
117C THR* 4.3 7.3 - - - +
118C ALA* 3.6 30.0 + - + +
132C TYR* 4.5 8.6 + - - +
133C LEU* 5.5 0.7 - - + -
339C ILE* 4.3 15.2 - - + +
340C THR* 3.8 5.8 - - - +
343C MET* 4.6 5.4 - - + -
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 5.1 6.4 + - - -
139B SER* 5.4 5.0 + - - -
405B GLU 5.8 2.7 - - - +
406B SER* 6.4 3.1 - - - -
85C ASN* 3.3 7.7 + - - +
86C GLN* 1.3 78.0 - - - +
88C GLN* 1.3 58.4 + - - +
90C ASP* 3.3 1.0 + - - +
91C ASP* 2.9 46.2 + - - +
340C THR* 3.7 25.7 + - + +
343C MET* 5.9 1.2 - - - +
347C ARG* 5.9 0.9 + - - -
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.0 27.9 - - + +
82C ASP* 4.1 18.6 + - - +
85C ASN* 3.0 41.6 + - - +
87C THR* 1.3 74.2 - - - +
89C LEU* 1.3 62.4 + - - +
91C ASP* 4.2 4.4 - - - +
92C THR* 2.6 42.8 + - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.3 8.1 - - + -
78C ILE* 3.7 40.8 - - + -
81C LEU* 4.5 8.3 - - + +
82C ASP 5.7 2.2 - - - +
85C ASN 3.0 14.8 + - - +
86C GLN* 3.1 23.3 + - - +
88C GLN* 1.3 77.9 - - - +
90C ASP* 1.3 64.4 + - - +
92C THR* 3.4 4.7 - - - -
93C LEU* 2.9 35.3 + - + +
113C VAL* 4.0 8.7 - - + +
114C SER* 4.1 2.9 - - - -
117C THR* 3.3 42.0 - - + +
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 2.9 24.5 + - - +
87C THR 4.1 0.4 - - - +
89C LEU* 1.3 77.0 - - - +
91C ASP* 1.3 58.6 + - - +
93C LEU* 3.3 11.2 + - - +
94C ARG* 3.0 27.4 + - - +
114C SER* 2.6 32.8 + - - -
338C THR* 3.5 24.5 + - - +
340C THR* 2.5 50.6 + - - +
341C GLN* 4.9 2.0 + - + -
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C THR* 2.9 38.5 + - - +
88C GLN* 4.2 4.4 - - - +
90C ASP* 1.3 76.3 - - - +
92C THR* 1.3 60.1 + - - +
94C ARG* 2.8 35.6 + - - +
95C GLU* 3.0 37.0 + - + +
340C THR* 4.9 8.1 - - - +
341C GLN* 5.8 3.6 - - - +
344C ARG* 5.9 2.1 - - - -
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLU* 3.6 37.7 - - + +
78C ILE* 4.5 5.6 - - + -
81C LEU* 3.9 22.8 - - + +
88C GLN* 2.6 30.4 + - - +
89C LEU 3.4 4.5 - - - -
91C ASP* 1.3 73.2 - - - +
93C LEU* 1.3 59.0 + - - +
95C GLU* 3.8 5.8 - - + +
96C LEU* 2.8 29.7 + - + +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 3.7 45.3 - - + -
78C ILE* 4.3 11.0 - - + -
89C LEU* 2.9 26.0 + - + +
90C ASP* 3.3 28.9 + - - +
92C THR* 1.3 75.2 - - - +
94C ARG* 1.3 63.2 + - - +
96C LEU* 4.4 6.1 - - + -
97C ASP* 3.0 24.4 + - - +
102C TYR* 3.8 2.8 - - - -
105C LEU* 3.7 5.4 - - + +
110C THR* 3.7 31.6 - - + +
113C VAL* 4.4 4.5 - - + -
114C SER* 4.2 6.7 - - - +
338C THR* 4.2 11.9 - - + -
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP 3.0 11.7 + - - +
91C ASP* 2.8 41.6 + - - +
92C THR 3.3 0.4 - - - -
93C LEU* 1.3 76.2 - - - +
95C GLU* 1.3 87.2 + - - +
97C ASP* 3.4 3.6 + - - +
98C GLY* 3.1 23.0 + - - -
99C THR 4.7 12.3 - - - +
102C TYR* 3.4 27.3 + - + +
341C GLN* 4.1 20.3 + - - +
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ASP* 3.0 24.0 + - + +
92C THR* 3.8 6.5 - - - +
94C ARG* 1.3 96.8 + - - +
96C LEU* 1.3 67.4 + - - +
98C GLY* 3.4 13.1 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C THR* 3.7 37.9 - - + +
74C ILE* 3.8 19.5 - - + -
77C GLU* 3.8 35.2 - - + +
78C ILE* 5.8 0.7 - - + -
92C THR 2.8 18.3 + - - +
93C LEU* 3.8 7.9 - - + +
95C GLU* 1.3 75.8 - - - +
97C ASP* 1.3 64.0 + - - +
98C GLY* 4.5 0.3 - - - -
104C ASN* 3.5 8.8 + - - -
105C LEU* 4.0 15.9 - - + -
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU 3.0 18.3 + - - +
94C ARG 3.5 4.4 - - - +
96C LEU* 1.3 76.2 - - - +
98C GLY* 1.3 58.1 + - - +
99C THR* 2.4 44.3 + - - +
102C TYR* 3.1 37.6 + - + -
104C ASN* 3.0 32.7 + - - +
105C LEU* 3.0 35.7 + - + +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG 3.1 9.9 + - - -
95C GLU* 3.4 13.3 + - - -
96C LEU 4.5 0.2 - - - -
97C ASP* 1.3 77.6 - - - +
99C THR* 1.3 61.8 + - - +
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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