Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 2Q1V
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 MET 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.3 4.3 - - + -
32A LEU* 3.6 24.9 - - + -
92A PHE* 4.7 2.5 - - + -
98A PHE* 4.8 0.4 - - + -
106A SER* 3.1 22.4 + - - +
107A ALA* 1.3 80.8 - - - +
109A TYR* 1.3 64.2 + - - +
110A ASP* 3.2 3.6 - - - -
111A LEU* 3.0 26.8 + - + +
112A CYS* 2.9 35.3 + - - -
115A MET* 4.3 12.3 - - + -
204A PHE* 4.0 17.5 - - + -
248A PDN 3.2 42.6 - - + +
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Residues in contact with TYR 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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100A GLU* 2.2 34.0 + - - -
103A MET* 3.5 42.1 + - + +
104A GLN* 3.4 32.3 - - + +
107A ALA 3.7 1.8 - - - -
108A MET* 1.3 75.9 - - - +
110A ASP* 1.3 67.7 + - - +
112A CYS* 3.1 7.1 + - - +
113A GLN* 2.9 58.4 + - + +
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Residues in contact with ASP 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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108A MET* 3.2 1.0 - - - -
109A TYR* 1.3 87.4 - - - +
111A LEU* 1.3 66.1 + - + +
113A GLN* 3.2 7.7 + - - +
114A GLY* 3.0 18.7 + - - -
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Residues in contact with LEU 111 (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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108A MET* 3.0 26.4 + - + +
110A ASP* 1.3 75.9 - - + +
112A CYS* 1.3 66.5 + - - +
114A GLY* 3.1 3.4 + - - +
115A MET* 2.9 29.2 + - - +
197A LEU* 4.6 6.0 - - + +
200A GLY* 3.8 30.7 - - - +
201A LEU* 4.0 22.9 - - + +
204A PHE* 3.7 40.6 - - + -
248A PDN 4.6 1.1 - - + -
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Residues in contact with CYS 112 (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 LEU* 3.6 27.4 - - + +
92A PHE* 5.2 0.2 - - - -
98A PHE* 4.3 6.5 - - - -
103A MET* 3.8 30.7 - - + -
106A SER* 3.9 16.6 - - - -
108A MET* 2.9 35.7 + - - -
109A TYR* 3.3 9.4 - - - +
111A LEU* 1.3 78.0 - - - +
113A GLN* 1.3 57.9 + - - +
115A MET* 3.3 4.2 + - - +
116A ARG* 2.9 29.0 + - - +
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Residues in contact with GLN 113 (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 GLU* 4.9 1.2 + - - -
103A MET* 4.0 15.2 - - - +
109A TYR* 2.9 58.0 + - + +
110A ASP* 3.7 7.6 - - - +
111A LEU 3.2 0.2 - - - -
112A CYS* 1.3 74.6 - - + +
114A GLY* 1.3 65.3 + - - +
116A ARG* 3.0 41.2 + - - +
117A GLN* 2.9 41.2 + - - +
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Residues in contact with GLY 114 (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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110A ASP 3.0 14.3 + - - -
111A LEU* 3.1 4.6 + - - -
113A GLN* 1.3 77.0 - - - +
115A MET* 1.3 62.0 + - - +
117A GLN* 3.3 27.0 + - - +
118A ILE* 3.5 12.0 + - - +
197A LEU* 3.8 18.7 - - - +
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Residues in contact with MET 115 (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 ALA* 4.8 7.2 - - + +
77A LEU* 3.6 30.2 - - + +
78A GLY* 4.8 4.5 - - - -
90A LEU* 4.2 6.3 - - + +
92A PHE* 4.2 15.9 - - + -
108A MET* 4.3 12.8 - - + -
111A LEU* 2.9 24.5 + - + +
112A CYS* 3.7 16.2 - - - +
114A GLY* 1.3 75.6 - - - +
116A ARG* 1.3 64.8 + - - +
118A ILE* 3.1 19.7 + - - +
119A SER* 3.4 5.4 + - - -
197A LEU* 4.3 11.4 - - + -
201A LEU* 4.0 28.3 - - + -
248A PDN 3.7 28.9 - - + -
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Residues in contact with ARG 116 (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 GLY 2.6 39.8 + - - +
88A GLN* 3.5 32.6 + - - +
89A MET* 4.7 3.4 - - - +
90A LEU* 3.8 16.8 - - + +
103A MET* 5.0 10.1 - - - -
112A CYS 2.9 18.1 + - - +
113A GLN* 3.0 39.8 + - - +
114A GLY 3.3 0.2 - - - -
115A MET* 1.3 76.1 - - - +
117A GLN* 1.3 57.7 + - - +
119A SER* 3.0 10.2 + - - -
120A GLN* 2.6 65.6 + - - +
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Residues in contact with GLN 117 (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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113A GLN* 2.9 36.0 + - - +
114A GLY* 3.4 14.5 - - - +
115A MET 3.2 0.4 - - - -
116A ARG* 1.3 73.7 - - - +
118A ILE* 1.3 67.3 + - + +
120A GLN* 3.3 23.0 + - - +
121A GLU* 3.0 26.3 + - - +
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Residues in contact with ILE 118 (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 ALA 4.8 7.4 - - - +
75A PHE* 4.5 4.7 - - + -
78A GLY* 4.4 7.4 - - - -
114A GLY 3.8 6.1 - - - +
115A MET* 3.1 9.1 + - - +
117A GLN* 1.3 77.9 - - + +
119A SER* 1.3 65.3 + - - +
121A GLU* 3.1 16.6 + - + +
122A PHE* 3.1 35.6 + - + -
190A LEU* 4.0 11.9 - - + -
193A SER* 3.9 20.2 - - - +
194A MET* 3.7 28.0 - - + -
197A LEU* 3.5 29.6 - - + -
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Residues in contact with SER 119 (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 GLY* 3.0 31.5 + - - -
81A SER* 3.2 14.6 - - - -
82A TYR* 3.1 16.5 + - - +
87A GLY* 3.3 14.6 - - - -
90A LEU* 5.5 0.2 - - - -
115A MET 3.4 4.0 + - - -
116A ARG* 3.0 17.9 + - - -
118A ILE* 1.3 81.0 - - - +
120A GLN* 1.3 58.8 + - - +
122A PHE* 3.1 15.6 + - - +
123A VAL* 3.1 16.5 + - - +
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Residues in contact with GLN 120 (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 ASN 5.7 0.2 - - - +
87A GLY* 4.0 7.0 - - - +
88A GLN* 5.0 1.2 - - - +
113A GLN* 5.3 0.2 + - - -
116A ARG* 2.6 58.7 + - - +
117A GLN* 3.5 32.9 - - - +
118A ILE 3.2 0.2 - - - -
119A SER* 1.3 73.4 - - - +
121A GLU* 1.3 65.3 + - - +
123A VAL* 3.3 11.4 + - + +
124A ARG* 2.9 26.7 + - - +
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Residues in contact with GLU 121 (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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117A GLN 3.0 15.8 + - - +
118A ILE* 3.1 10.3 + - + +
120A GLN* 1.3 77.7 - - - +
122A PHE* 1.3 67.7 + - - +
124A ARG* 3.0 45.8 + - - +
125A LEU* 2.9 36.3 + - + +
190A LEU* 3.9 27.0 - - + +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.4 43.7 - + - -
78A GLY* 3.4 23.6 - - - -
79A TRP* 3.2 35.2 - + + -
82A TYR* 3.6 21.9 - + + -
118A ILE* 3.1 16.0 + - + -
119A SER 3.1 8.2 + - - +
121A GLU* 1.3 76.6 - - - +
123A VAL* 1.3 52.8 + - - +
126A GLN* 2.7 30.3 + - - -
127A VAL* 3.2 39.4 + - + -
132A PHE* 4.2 5.4 - + - -
135A MET* 5.1 0.2 - - + -
190A LEU* 3.6 24.9 - - + -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.5 25.4 - - + -
86A ASN* 3.5 44.0 - - - +
87A GLY 4.3 0.2 - - - +
119A SER 3.1 14.6 + - - +
120A GLN* 3.4 13.0 - - + +
121A GLU 3.1 0.4 - - - -
122A PHE* 1.3 74.4 - - - +
124A ARG* 1.3 67.1 + - - +
126A GLN* 2.8 32.3 + - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLN 2.9 18.0 + - - +
121A GLU* 3.0 39.1 + - - +
123A VAL* 1.3 77.8 - - - +
125A LEU* 1.3 89.3 + - - +
126A GLN* 3.6 3.8 + - - +
186A GLN* 4.1 18.4 - - - +
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Residues in contact with LEU 125 (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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121A GLU* 2.9 24.2 + - - +
124A ARG* 1.3 108.3 - - - +
126A GLN* 1.3 71.4 + - - +
127A VAL* 4.0 10.1 - - + -
183A ARG* 2.7 36.3 + - - +
186A GLN* 3.9 44.4 - - + +
187A LEU* 4.1 20.9 - - + -
190A LEU* 4.5 15.3 - - + -
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Residues in contact with GLN 126 (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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82A TYR* 3.5 21.4 + - - -
86A ASN* 5.5 1.4 + - - -
122A PHE 2.7 15.3 + - - -
123A VAL* 2.8 36.6 + - - +
124A ARG 4.5 3.6 - - - +
125A LEU* 1.3 77.5 - - - +
127A VAL* 1.3 64.1 + - - +
128A THR* 3.4 7.3 + - - +
183A ARG* 3.3 6.4 + - - -
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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