Contacts of the helix formed by residues 85 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.4 30.6 + - - +
83A ALA 4.9 1.1 - - - -
84A PHE* 1.3 74.4 - - - +
86A GLN* 1.3 61.8 + - - +
87A THR* 3.6 8.3 + - - -
88A GLN* 3.0 44.9 + - + +
89A LEU* 3.0 22.1 + - - +
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Residues in contact with GLN 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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83A ALA 4.9 2.3 + - - +
84A PHE 3.3 8.4 + - - +
85A ASN* 1.3 74.2 + - - +
87A THR* 1.3 57.6 + - - +
89A LEU* 3.2 12.2 + - - +
90A ASP* 2.8 59.2 + - - +
114A SER* 3.1 30.1 + - - -
117A THR* 4.3 7.0 - - - +
118A ALA* 3.6 29.6 + - - +
132A TYR* 4.5 13.4 + - + +
133A LEU* 5.7 3.1 - - + -
339A ILE* 4.1 13.0 - - + +
340A THR* 3.7 5.8 - - - +
343A MET* 5.0 5.4 - - + -
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Residues in contact with THR 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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85A ASN* 3.2 7.7 + - - +
86A GLN* 1.3 77.0 - - - +
88A GLN* 1.3 58.2 + - - +
90A ASP* 3.3 1.4 + - - +
91A ASP* 2.9 47.0 + - - +
340A THR* 3.7 24.8 + - + +
343A MET* 5.7 2.3 - - - +
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Residues in contact with GLN 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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81A LEU* 3.9 27.4 - - + +
82A ASP* 4.1 16.8 + - - +
85A ASN* 3.0 39.7 + - - +
87A THR* 1.3 73.9 - - - +
89A LEU* 1.3 60.5 + - - +
91A ASP* 4.1 5.3 - - - +
92A THR* 2.7 40.4 + - - +
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Residues in contact with LEU 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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4A ILE* 4.2 8.1 - - + -
78A ILE* 3.7 42.6 - - + -
81A LEU* 4.5 9.9 - - + -
82A ASP 5.7 3.1 - - - +
85A ASN 3.0 14.1 + - - +
86A GLN* 3.5 18.2 - - - +
88A GLN* 1.3 76.3 - - - +
90A ASP* 1.3 69.8 + - - +
92A THR* 3.1 7.7 + - - -
93A LEU* 2.9 37.3 + - + +
113A VAL* 4.2 1.3 - - + +
114A SER* 4.1 8.7 - - - -
117A THR* 3.4 37.5 - - + +
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Residues in contact with ASP 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 GLN* 2.8 26.9 + - - +
87A THR 4.0 0.2 - - - +
89A LEU* 1.3 73.4 - - - +
91A ASP* 1.3 63.6 + - - +
93A LEU* 3.3 11.3 + - - +
94A ARG* 3.1 21.5 + - - +
102A TYR* 4.1 0.3 + - - -
114A SER* 2.6 34.3 + - - -
338A THR* 3.5 23.1 + - - +
340A THR* 2.5 51.1 + - + +
341A GLN* 4.7 1.8 + - + -
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Residues in contact with ASP 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 THR* 2.9 37.7 + - - +
88A GLN* 4.1 5.7 - - - +
90A ASP* 1.3 75.2 - - - +
92A THR* 1.3 65.2 + - - +
94A ARG* 3.0 33.4 + - - +
95A GLU* 3.0 32.2 + - - +
340A THR* 4.8 8.5 - - - +
341A GLN* 5.9 3.1 - - - +
344A ARG* 6.0 1.4 - - - -
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Residues in contact with THR 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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77A GLU* 3.5 35.7 - - + +
78A ILE* 4.6 6.5 - - + -
81A LEU* 4.0 23.6 - - + +
88A GLN* 2.7 28.6 + - - +
89A LEU 3.4 4.9 - - - -
91A ASP* 1.3 74.0 - - - +
93A LEU* 1.3 59.6 + - - +
95A GLU* 3.4 6.4 + - + +
96A LEU* 2.8 33.1 + - + +
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Residues in contact with LEU 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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74A ILE* 3.5 45.5 - - + -
78A ILE* 4.3 10.1 - - + -
89A LEU* 2.9 27.5 + - + +
90A ASP* 3.6 27.4 - - - +
92A THR* 1.3 77.2 - - - +
94A ARG* 1.3 56.9 + - - +
96A LEU* 3.6 7.2 - - + +
97A ASP* 2.9 30.3 + - - +
102A TYR* 4.2 2.7 - - - +
105A LEU* 3.7 4.5 - - + +
110A THR* 3.8 34.8 - - + +
113A VAL* 4.4 4.0 - - + -
114A SER 4.3 6.1 - - - +
338A THR* 4.3 9.4 - - + -
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Residues in contact with ARG 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 ASP 3.1 10.9 + - - +
91A ASP* 3.0 39.7 + - - +
93A LEU* 1.3 74.7 - - - +
95A GLU* 1.3 89.8 + - - +
97A ASP* 3.4 4.2 + - - +
98A GLY* 2.8 30.5 + - - -
99A THR 4.5 11.8 - - - +
102A TYR* 3.4 27.5 + - + +
341A GLN* 4.1 19.5 + - - +
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Residues in contact with GLU 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 ASP* 3.0 19.1 + - - +
92A THR* 3.7 7.2 - - + +
94A ARG* 1.3 106.5 + - - +
96A LEU* 1.3 66.6 + - - +
98A GLY* 3.3 13.5 + - - +
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Residues in contact with LEU 96 (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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73A THR* 3.9 30.1 - - + +
74A ILE* 3.9 14.1 - - + -
77A GLU* 3.9 45.7 + - + +
78A ILE* 5.8 0.2 - - + -
92A THR* 2.8 21.4 + - + +
93A LEU* 3.6 9.2 - - + +
95A GLU* 1.3 75.0 - - - +
97A ASP* 1.3 64.6 + - - +
98A GLY* 4.4 0.2 - - - -
104A ASN* 3.5 8.7 + - - +
105A LEU* 3.9 18.2 - - + -
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Residues in contact with ASP 97 (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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93A LEU 2.9 14.5 + - - +
94A ARG 3.5 7.4 - - - +
96A LEU* 1.3 77.7 - - - +
98A GLY* 1.3 56.1 + - - +
99A THR* 2.5 46.7 + - - +
102A TYR* 3.2 32.7 + - + -
104A ASN* 3.1 38.2 + - - +
105A LEU* 3.0 34.3 + - + +
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Residues in contact with GLY 98 (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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94A ARG 2.8 17.4 + - - -
95A GLU* 3.3 14.2 + - - -
96A LEU 4.4 0.2 - - - -
97A ASP* 1.3 72.3 - - - +
99A THR* 1.3 61.4 + - - +
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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