Contacts of the helix formed by residues 124 - 141 (chain B) in PDB entry 2QY7
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 GLN 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TRP* 3.6 58.0 - - + +
116B PHE* 2.9 16.9 + - + -
118B ASP* 3.2 26.2 + - + +
122B LYS* 3.3 18.1 + - - +
123B ASP* 1.3 72.7 - - - +
125B GLY* 1.3 64.2 + - - +
126B ILE 3.2 2.2 - - - -
127B ASN* 3.2 35.0 + - - +
128B ILE* 4.0 5.4 + - - +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 3.8 16.6 - - - +
116B PHE* 2.9 25.4 + - - +
123B ASP* 3.1 4.0 + - - -
124B GLN* 1.3 74.9 - - - +
126B ILE* 1.3 62.1 + - - +
128B ILE* 3.0 15.4 + - - +
129B ARG* 3.0 29.4 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.0 36.2 + - + +
125B GLY* 1.3 76.4 - - - +
127B ASN* 1.3 69.0 + - - +
129B ARG* 3.4 28.6 - - + +
130B GLN* 3.0 65.3 + - + +
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 4.2 14.0 - - + -
80B TYR* 3.6 30.2 + - + +
123B ASP 4.5 2.2 + - - -
124B GLN* 3.2 36.4 + - - +
125B GLY 3.2 0.4 - - - -
126B ILE* 1.3 84.0 - - - +
128B ILE* 1.3 58.1 + - + +
130B GLN* 4.1 10.9 + - - +
131B LYS* 3.1 31.2 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.4 16.4 - - + +
79B VAL* 3.6 22.0 - - + -
80B TYR* 3.3 44.4 - - + +
83B LEU* 3.9 12.7 - - + +
111B LEU* 4.2 11.2 - - + +
114B TYR* 3.7 40.8 - - + -
124B GLN 4.3 8.3 - - - +
125B GLY 3.0 7.6 + - - +
127B ASN* 1.3 75.1 - - - +
129B ARG* 1.3 61.0 + - - +
131B LYS* 3.3 0.7 + - - -
132B VAL* 2.9 29.1 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU 4.0 8.1 - - - +
112B GLU 3.2 26.2 - - - +
113B ASN* 4.0 4.3 - - - +
114B TYR* 2.8 38.5 + - - +
115B HIS* 4.5 6.9 + - - +
116B PHE 4.9 0.2 - - - +
123B ASP* 3.1 25.1 + - - -
125B GLY* 3.0 26.1 + - - +
126B ILE* 3.4 27.0 - - + +
128B ILE* 1.3 75.6 - - - +
130B GLN* 1.3 64.8 + - + +
132B VAL* 3.6 2.2 - - - +
133B LYS* 3.2 40.8 + - - +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.0 53.6 + - + +
127B ASN* 4.1 10.7 + - - +
129B ARG* 1.3 79.7 - - + +
131B LYS* 1.3 61.9 + - - +
133B LYS* 3.8 6.2 - - + +
134B GLU* 3.2 31.8 + - + +
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Residues in contact with LYS 131 (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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80B TYR* 4.3 14.4 - - + +
83B LEU* 3.8 28.3 - - + -
84B LEU* 3.9 26.1 - - + +
87B ALA* 3.6 32.2 - - - +
127B ASN 3.1 19.8 + - - +
128B ILE 4.0 2.2 - - - +
130B GLN* 1.3 76.8 - - - +
132B VAL* 1.3 56.7 + - - +
134B GLU* 3.4 10.2 + - + +
135B LEU* 3.0 29.1 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.8 17.9 - - + +
108B LEU* 3.1 50.7 - - + +
111B LEU* 3.9 29.8 - - + +
112B GLU* 4.0 11.4 - - + +
128B ILE 2.9 20.8 + - - +
129B ARG 3.6 6.7 - - - +
131B LYS* 1.3 73.3 - - - +
133B LYS* 1.3 63.9 + - - +
135B LEU* 3.6 5.0 - - + +
136B VAL* 2.8 37.2 + - + +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 3.8 51.7 + - + +
129B ARG* 3.2 26.8 + - - +
130B GLN* 3.8 6.1 - - - +
131B LYS 3.3 0.2 - - - -
132B VAL* 1.3 77.3 - - - +
134B GLU* 1.3 60.5 + - - +
136B VAL* 3.4 5.5 + - - +
137B GLU* 3.0 46.1 + - - +
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Residues in contact with GLU 134 (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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130B GLN* 3.2 21.1 + - + +
131B LYS* 3.7 13.2 - - + +
132B VAL 3.3 0.2 - - - -
133B LYS* 1.3 77.5 - - - +
135B LEU* 1.3 57.3 + - - +
137B GLU* 3.5 22.1 + - - +
138B PHE* 3.0 29.6 + - - +
144B ARG* 5.0 2.6 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.7 40.2 - - + +
86B LEU* 3.7 28.7 - - + -
87B ALA* 3.9 21.8 - - + +
90B ILE* 3.7 24.5 - - + -
108B LEU* 4.6 7.2 - - + -
131B LYS* 3.0 19.7 + - + +
132B VAL* 3.2 7.8 + - + +
134B GLU* 1.3 75.8 - - - +
136B VAL* 1.3 52.9 + - - +
138B PHE* 3.4 13.0 + - + +
139B ALA* 2.8 36.1 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.4 9.0 - - + -
108B LEU* 3.9 26.9 - - + -
109B ARG* 3.9 36.3 - - + +
112B GLU* 4.2 9.2 - - - +
132B VAL* 2.8 24.4 + - + +
133B LYS* 3.7 5.6 - - - +
135B LEU* 1.3 73.2 - - - +
137B GLU* 1.3 62.9 + - + +
139B ALA* 3.4 0.7 + - - +
140B GLN* 3.0 51.9 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS* 3.0 34.3 + - - +
134B GLU* 3.6 25.1 - - - +
136B VAL* 1.3 78.9 - - + +
138B PHE* 1.3 61.7 + - - +
140B GLN* 3.6 5.7 + - - +
141B ASP* 3.3 24.6 + - - +
144B ARG* 4.4 8.2 + - - +
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Residues in contact with PHE 138 (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 ALA* 5.3 1.3 - - - -
90B ILE* 3.6 31.6 - - + -
91B ARG* 3.7 30.5 - - + -
134B GLU 3.0 18.0 + - - +
135B LEU* 3.6 13.5 - - + +
137B GLU* 1.3 76.5 - - - +
139B ALA* 1.3 62.9 + - - +
141B ASP* 3.1 19.7 + - - +
144B ARG* 3.5 40.1 - - + +
145B LEU* 3.7 31.9 - - + +
148B GLU* 3.8 35.2 - - + -
149B ARG* 5.7 0.2 - - + -
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Residues in contact with ALA 139 (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 ILE* 4.2 20.0 - - + -
98B VAL* 6.4 0.2 - - + -
101B ALA* 4.6 9.0 - - + -
102B ARG* 3.5 22.5 + - + +
105B ILE* 3.9 22.7 - - + -
108B LEU* 5.3 2.2 - - + -
135B LEU 2.8 20.0 + - - +
138B PHE* 1.3 74.5 - - - +
140B GLN* 1.3 59.8 + - - +
145B LEU* 3.4 24.1 - - + +
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Residues in contact with GLN 140 (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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102B ARG* 5.8 1.1 - - + +
105B ILE* 3.8 30.6 - - + +
106B TYR* 5.1 7.7 + - - -
109B ARG* 4.8 8.0 - - - +
136B VAL* 3.0 37.3 + - - +
137B GLU* 4.0 5.7 + - - +
138B PHE 3.2 0.4 - - - -
139B ALA* 1.3 77.6 - - - +
141B ASP* 1.3 58.2 + - - +
142B ASP* 3.4 6.8 + - - +
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Residues in contact with ASP 141 (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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137B GLU 3.3 17.1 + - - +
138B PHE* 3.1 9.3 + - - +
139B ALA 4.7 0.4 - - - -
140B GLN* 1.3 75.8 - - - +
142B ASP* 1.3 57.9 + - - +
143B ASP* 3.5 10.9 + - - +
144B ARG* 3.2 41.0 + - + +
145B LEU* 2.9 30.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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