Contacts of the helix formed by residues 93 - 110 (chain A) in PDB entry 2QNJ
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLN 4.1 1.6 + - - -
92A LEU* 1.3 74.9 - - - +
94A PRO* 1.4 77.1 - - + +
95A THR* 3.0 20.4 + - - -
96A SER* 3.0 29.2 + - - -
97A LEU* 3.1 10.5 + - - +
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Residues in contact with PRO 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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93A ASN* 1.4 87.7 - - + +
95A THR* 1.3 57.7 + - - +
97A LEU* 3.1 15.2 - - + +
98A GLN* 2.9 45.0 + - - +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 3.0 12.6 + - - -
94A PRO* 1.3 79.8 - - - +
96A SER* 1.3 58.2 + - - +
98A GLN* 3.2 18.0 + - - +
99A LYS* 3.0 44.0 + - + +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.0 21.9 - - - +
93A ASN* 3.0 25.8 + - - -
95A THR* 1.3 74.4 - - - +
97A LEU* 1.3 60.4 + - - +
99A LYS* 3.4 7.0 + - - +
100A LEU* 2.9 24.9 + - - +
202A GLU* 2.8 31.5 + - - -
203A PHE* 3.3 12.4 - - - -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 4.2 25.1 - - + +
92A LEU* 3.5 37.0 - - + +
93A ASN 3.1 10.4 + - - +
94A PRO* 3.1 16.4 - - + +
96A SER* 1.3 76.4 - - - +
98A GLN* 1.3 63.9 + - + +
100A LEU* 3.1 9.1 + - + +
101A PHE* 3.0 48.9 + - + -
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Residues in contact with GLN 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 PRO* 2.9 35.0 + - - +
95A THR* 3.2 15.3 + - - +
97A LEU* 1.3 73.9 - - + +
99A LYS* 1.3 65.9 + - + +
101A PHE* 3.2 10.4 + - + +
102A ARG* 3.0 23.4 + - - +
105A ARG* 4.5 3.5 + - - -
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Residues in contact with LYS 99 (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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95A THR* 3.0 31.7 + - + +
96A SER* 3.6 7.4 - - - +
98A GLN* 1.3 75.2 - - + +
100A LEU* 1.3 64.1 + - - +
102A ARG* 3.3 11.6 + - - +
103A GLU* 3.2 28.0 + - - +
200A SER* 3.4 31.7 - - - +
202A GLU* 4.0 14.9 + - - +
203A PHE* 4.2 11.7 - - + -
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Residues in contact with LEU 100 (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 ILE* 4.1 20.9 - - + -
89A LYS* 4.6 7.6 - - + -
92A LEU* 3.9 22.2 - - + -
96A SER 2.9 14.1 + - - +
97A LEU* 3.2 18.4 - - + +
99A LYS* 1.3 76.1 - - - +
101A PHE* 1.3 67.8 + - + +
103A GLU* 3.3 9.3 + - + +
104A VAL* 3.1 21.3 + - + +
128A LEU* 3.9 29.8 - - + -
130A LEU* 5.2 3.4 - - + -
203A PHE* 3.7 34.2 - - + -
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Residues in contact with PHE 101 (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 LYS* 4.5 12.6 - - - -
97A LEU* 3.0 45.6 + - + -
98A GLN* 3.2 8.7 + - + +
100A LEU* 1.3 79.7 - - + +
102A ARG* 1.3 60.5 + - - +
104A VAL* 3.1 15.4 + - + +
105A ARG* 2.9 34.1 + - - +
123A GLU* 3.9 31.2 - - - -
128A LEU* 4.8 13.0 - - + -
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Residues in contact with ARG 102 (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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98A GLN 3.0 11.6 + - - +
99A LYS* 3.6 14.8 - - - +
100A LEU 3.3 0.2 - - - -
101A PHE* 1.3 74.5 - - - +
103A GLU* 1.3 66.9 + - + +
105A ARG* 3.0 42.3 + - - +
106A ILE* 3.0 45.1 + - + +
198A GLY 5.8 1.7 + - - -
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Residues in contact with GLU 103 (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 LYS* 5.1 2.6 + - - -
99A LYS* 3.2 15.5 + - - +
100A LEU* 3.5 11.0 - - + +
101A PHE 3.2 0.2 - - - -
102A ARG* 1.3 80.5 - - + +
104A VAL* 1.3 62.4 + - + +
106A ILE* 3.5 4.1 + - + +
107A MET* 3.2 28.6 + - - +
130A LEU* 6.2 0.9 - - + -
198A GLY 5.3 0.2 - - - +
199A PHE* 3.2 51.9 - - + +
200A SER* 2.8 42.8 + - - +
203A PHE* 3.9 24.8 - - - +
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Residues in contact with VAL 104 (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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100A LEU* 3.1 14.3 + - + +
101A PHE* 3.6 16.4 - - + +
102A ARG 3.1 0.6 - - - -
103A GLU* 1.3 76.3 - - + +
105A ARG* 1.3 64.6 + - - +
106A ILE 3.3 0.5 + - - -
107A MET* 3.4 8.2 + - - +
108A LYS* 3.3 46.6 + - - +
118A LEU* 5.1 3.4 - - + -
121A VAL* 4.7 8.5 - - + -
128A LEU* 4.3 11.2 - - + -
130A LEU* 3.6 43.5 - - + -
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Residues in contact with ARG 105 (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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98A GLN 4.5 4.0 + - - -
101A PHE* 2.9 15.3 + - - +
102A ARG* 3.0 65.2 + - - +
104A VAL* 1.3 76.0 - - - +
106A ILE* 1.3 64.7 + - + +
108A LYS* 3.1 23.6 + - + +
109A ILE* 3.2 23.9 + - + +
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Residues in contact with ILE 106 (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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102A ARG* 3.0 48.6 + - + +
103A GLU* 3.9 9.0 - - + +
105A ARG* 1.3 77.1 - - + +
107A MET* 1.3 66.9 + - - +
109A ILE* 3.4 10.3 + - + +
110A LEU* 3.2 35.5 + - + +
174A ILE* 3.8 31.9 - - + -
197A PHE 4.3 4.3 - - - +
198A GLY* 4.0 19.7 - - - +
199A PHE* 3.8 18.8 - - + -
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Residues in contact with MET 107 (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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103A GLU 3.2 16.7 + - - +
104A VAL* 3.8 8.3 - - - +
105A ARG 3.3 0.2 - - - -
106A ILE* 1.3 77.2 - - - +
108A LYS* 1.3 62.9 + - - +
110A LEU* 3.3 22.9 - - - +
111A ASN* 4.6 1.7 + - - +
116A VAL* 3.8 38.3 - - + +
118A LEU* 4.0 37.8 + - + +
130A LEU* 4.7 12.3 - - - -
132A MET* 3.4 34.8 - - + -
199A PHE* 3.5 24.7 - - + -
354A TYR* 4.7 0.7 + - - -
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Residues in contact with LYS 108 (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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104A VAL* 3.3 36.7 - - + +
105A ARG* 3.1 14.2 + - + +
107A MET* 1.3 78.3 - - - +
109A ILE* 1.3 60.6 + - + +
111A ASN* 3.3 9.9 - - - +
118A LEU* 4.2 9.6 - - + -
121A VAL* 4.7 6.5 - - - +
353A LYS 5.8 1.6 + - - -
354A TYR* 3.3 56.8 + - + +
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Residues in contact with ILE 109 (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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105A ARG* 3.2 21.9 + - + +
106A ILE* 3.7 15.7 - - + +
107A MET 3.3 0.2 - - - -
108A LYS* 1.3 77.8 - - + +
110A LEU* 1.3 68.6 + - + +
111A ASN* 3.3 8.5 + - - +
168A TYR* 3.4 6.9 + - - -
172A LYS* 3.9 39.2 - - + -
174A ILE* 4.9 11.0 - - + -
321A GLU* 3.9 7.4 - - - +
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Residues in contact with LEU 110 (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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106A ILE* 3.2 34.5 + - + +
107A MET* 3.3 15.1 + - - +
109A ILE* 1.3 82.2 - - + +
111A ASN* 1.3 69.2 + - - +
112A HIS 4.2 0.7 - - - -
115A ILE* 4.3 26.5 - - + +
116A VAL 5.2 3.5 - - - +
117A LYS* 5.2 4.0 - - - +
168A TYR* 3.7 24.0 - - + -
169A CYS* 4.2 23.3 - - - -
172A LYS* 4.4 9.2 - - + -
174A ILE* 4.2 18.6 - - + -
197A PHE* 4.4 11.7 - - + +
199A PHE* 5.9 0.4 - - + -
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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