Contacts of the helix formed by residues 141 - 154 (chain B) in PDB entry 1Q90
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 ASP 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PHE* 4.0 15.9 - - + -
136B TYR 3.6 11.8 - - - +
139B PRO* 3.7 13.8 - - + +
140B TRP* 1.3 78.7 - - - +
142B GLN* 1.3 66.2 + - - +
143B VAL* 3.1 25.8 + - - +
144B GLY 3.2 15.2 + - - -
145B TYR* 2.7 22.6 + - - +
63D GLY* 4.1 16.0 - - - +
64D GLU 3.2 18.1 + - - +
65D PRO* 4.1 1.1 - - - -
66D ALA* 3.6 3.4 - - - +
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Residues in contact with GLN 142 (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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15A ALA 4.3 10.6 - - - +
141B ASP* 1.3 71.0 - - - +
143B VAL* 1.3 66.4 + - + +
146B TRP* 3.0 49.8 + - - +
64D GLU* 2.9 34.0 + - + +
65D PRO 3.3 13.7 - - - +
66D ALA* 3.3 4.2 - - - +
67D ASN* 2.5 40.0 - - + +
70D ALA 2.8 21.3 - - - +
72D PRO* 3.6 20.8 - - + +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 5.8 6.7 - - + -
141B ASP* 3.2 12.4 + - - +
142B GLN* 1.3 78.3 - - + +
144B GLY* 1.3 71.8 + - - +
145B TYR 2.9 0.7 + - - -
146B TRP* 3.8 0.3 - - - -
147B ALA* 2.9 23.0 + - + +
72D PRO* 5.3 4.5 - - + -
74D GLU 6.0 1.1 - - - +
75D ILE* 4.2 15.9 - - + -
76D LEU 4.7 5.2 - - - +
78D GLU* 5.4 4.7 - - - +
920D TDS 3.9 19.6 - - - +
1G MET* 4.3 32.3 - - + +
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Residues in contact with GLY 144 (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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136B TYR* 3.1 33.9 - - - -
137B SER* 4.0 5.8 - - - -
141B ASP* 3.2 10.8 + - - -
143B VAL* 1.3 82.5 - - - +
145B TYR* 1.3 64.6 + - - +
147B ALA* 3.4 7.9 - - - +
148B VAL* 3.0 24.9 + - - +
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Residues in contact with TYR 145 (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 SER* 4.9 0.2 - - - +
140B TRP* 3.7 33.0 - + + +
141B ASP 2.7 22.9 + - - +
142B GLN 3.6 3.6 - - - +
143B VAL 2.9 0.4 + - - -
144B GLY* 1.3 71.7 - - - +
146B TRP* 1.3 104.9 + + - +
148B VAL* 2.6 30.9 + - - +
149B LYS* 2.9 18.3 + - + +
175B VAL* 3.6 37.6 + - + +
66D ALA* 3.5 26.2 - - + -
68D PRO* 3.2 35.8 + - + +
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Residues in contact with TRP 146 (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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142B GLN* 3.0 39.8 + - - +
143B VAL 4.0 1.1 - - - +
145B TYR* 1.3 93.8 - + - +
147B ALA* 1.3 61.9 + - - +
149B LYS* 3.2 23.0 + - + +
150B ILE* 2.8 31.3 + - + +
138C GLY 4.0 6.1 - - - -
139C CYS* 3.9 9.6 - - - -
140C VAL* 3.3 34.5 - - + -
67D ASN 3.5 17.0 + - - -
68D PRO* 3.7 14.1 - - + -
70D ALA 3.1 20.2 + - - -
71D THR* 3.1 38.4 - - + -
72D PRO* 3.3 14.6 - - + -
75D ILE* 4.3 16.4 - - + -
920D TDS 4.7 0.9 - - - -
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Residues in contact with ALA 147 (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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133B VAL* 5.6 6.5 - - + +
136B TYR* 5.8 3.8 - - + -
143B VAL* 2.9 17.7 + - + +
144B GLY* 3.4 10.5 - - - +
146B TRP* 1.3 76.6 - - - +
148B VAL* 1.3 63.5 - - + +
150B ILE* 3.3 0.9 + - - +
151B VAL* 2.9 31.1 + - + +
78D GLU* 5.1 3.1 - - - +
920D TDS 2.9 42.9 - - - +
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Residues in contact with VAL 148 (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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133B VAL* 5.2 4.9 - - + +
137B SER* 3.2 28.5 - - - -
140B TRP* 5.2 4.0 - - + -
144B GLY 3.0 16.8 + - - +
145B TYR* 2.6 16.7 + - - +
147B ALA* 1.3 70.4 - - + +
149B LYS* 1.3 65.7 + - - +
151B VAL* 4.9 2.5 - - - -
152B THR* 2.8 32.0 + - - +
175B VAL* 4.0 15.7 - - + -
179B THR* 3.6 30.7 - - + -
183B PHE* 4.0 22.7 - - + -
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Residues in contact with LYS 149 (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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145B TYR* 2.9 16.0 + - + +
146B TRP* 3.4 32.1 - - + +
148B VAL* 1.3 75.7 - - - +
150B ILE* 1.3 65.7 + - + +
152B THR* 3.0 19.3 - - - +
153B GLY 3.1 3.3 + - - -
170B ARG* 3.3 32.7 + - - +
174B GLY* 5.9 0.9 - - - -
175B VAL* 3.8 19.9 - - + +
133C VAL* 4.0 18.0 - - - +
137C LEU 3.7 2.3 - - - +
138C GLY* 2.7 48.2 + - - +
140C VAL* 5.5 2.2 - - - +
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Residues in contact with ILE 150 (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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146B TRP* 2.8 23.2 + - + +
147B ALA 3.8 2.9 - - - +
149B LYS* 1.3 69.4 - - + +
151B VAL* 1.3 72.4 + - - +
153B GLY* 2.8 12.5 + - - -
154B VAL* 3.2 11.1 + - + +
137C LEU* 3.5 33.2 - - + +
139C CYS* 3.3 37.7 - - - +
154C CYS* 3.5 11.7 - - + -
155C HIS* 4.3 1.8 - - + -
75D ILE* 5.1 2.7 - - + -
920D TDS 3.6 55.6 - - + +
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Residues in contact with VAL 151 (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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133B VAL* 4.2 23.8 - - + -
147B ALA 2.9 23.7 + - - +
148B VAL* 4.1 1.6 - - - +
150B ILE* 1.3 75.8 - - - +
152B THR* 1.3 57.1 - - - +
153B GLY 2.7 11.3 + - - -
154B VAL* 3.0 24.8 + - - +
155B PRO* 3.4 3.8 - - - +
169B LEU* 6.3 0.7 - - + -
183B PHE* 6.0 3.4 - - + -
910D CLA 4.1 18.6 - - + -
920D TDS 3.5 67.0 - - + +
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Residues in contact with THR 152 (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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148B VAL* 2.8 37.6 + - - +
149B LYS* 3.0 14.8 - - - +
151B VAL* 1.3 74.4 - - - +
153B GLY* 1.3 57.6 + - - +
155B PRO* 3.6 8.1 - - - +
166B VAL* 3.7 19.4 - - - +
169B LEU* 3.4 28.6 + - - +
170B ARG* 2.8 49.4 - - + +
175B VAL* 4.0 3.6 - - + -
179B THR* 5.0 0.2 - - - +
183B PHE* 4.7 9.1 - - - -
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Residues in contact with GLY 153 (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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149B LYS 3.1 5.3 + - - -
150B ILE 2.8 10.0 + - - -
151B VAL 2.7 5.1 + - - -
152B THR* 1.3 71.6 - - - +
154B VAL* 1.3 52.8 + - - -
155B PRO* 2.6 20.2 - - - +
156B ASP* 2.8 25.3 + - - +
166B VAL* 3.7 5.7 - - - +
170B ARG* 3.4 17.7 - - - -
137C LEU* 4.0 8.7 - - - -
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Residues in contact with VAL 154 (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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150B ILE* 3.2 10.2 + - + +
151B VAL* 3.0 15.9 + - - +
153B GLY* 1.3 71.2 - - - +
155B PRO* 1.3 71.5 - - + +
156B ASP* 3.2 2.8 + - - +
157B ALA* 3.2 20.8 + - - +
137C LEU* 3.4 33.9 - - + +
88D LEU* 5.5 0.7 - - + -
94D LYS* 5.3 0.2 - - - -
98D VAL* 4.0 21.5 - - + +
101D MET* 3.7 27.1 - - + -
920D TDS 4.1 23.8 - - + -
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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