Contacts of the helix formed by residues 139 - 154 (chain D) in PDB entry 3Q37
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 ARG 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D GLU* 2.9 29.3 + - - +
137D ALA* 3.6 26.2 - - + +
138D GLY* 1.3 78.4 - - - +
140D THR* 1.3 65.0 + - - +
141D ALA 3.4 2.7 - - - -
142D ALA* 3.9 24.5 - - + +
143D VAL* 2.9 48.1 + - + +
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Residues in contact with THR 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU* 2.8 40.9 + - - +
134D GLU 4.0 1.6 + - - -
135D ARG* 3.7 23.3 + - - +
138D GLY 3.5 3.4 + - - -
139D ARG* 1.3 76.8 - - - +
141D ALA* 1.3 65.7 + - - +
143D VAL* 3.9 0.5 - - - +
144D VAL* 3.1 33.1 + - + +
187D VAL* 4.0 25.4 - - + -
190D LEU* 4.6 8.1 - - + -
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY 5.3 0.8 + - - -
139D ARG 3.4 0.4 - - - -
140D THR* 1.3 80.2 - - - +
142D ALA* 1.3 63.2 + - - +
144D VAL* 4.2 6.7 - - - -
145D LEU* 3.0 42.8 + - + +
190D LEU* 4.3 19.7 - - + -
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ARG* 3.4 36.4 + - + +
140D THR 3.3 0.2 - - - -
141D ALA* 1.3 78.9 - - - +
143D VAL* 1.3 61.1 + - - +
145D LEU* 4.6 1.1 - - - +
146D THR* 2.7 33.4 + - - +
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLY 4.1 1.6 - - - +
130D GLU* 3.9 12.8 - - + -
134D GLU* 3.5 47.6 - - + +
139D ARG* 2.9 44.9 + - - +
140D THR 4.0 2.0 - - - +
142D ALA* 1.3 74.0 - - - +
144D VAL* 1.3 59.1 + - - +
146D THR* 3.7 3.9 - - - -
147D GLN* 2.9 54.5 + - + +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D VAL* 4.3 13.1 - - + +
129D GLY* 3.8 35.0 - - - +
130D GLU* 4.0 13.0 - - + +
140D THR* 3.1 22.1 + - + +
141D ALA 3.8 0.9 - - - +
143D VAL* 1.3 75.3 - - - +
145D LEU* 1.3 60.5 + - - +
147D GLN* 3.4 11.5 + - - +
148D LEU* 2.9 27.4 + - - +
167D TYR* 4.1 9.2 - - + -
187D VAL* 4.5 7.2 - - + -
190D LEU* 3.8 27.1 - - + -
191D LEU* 4.1 9.8 - - + +
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA* 3.0 29.7 + - + +
142D ALA* 4.6 0.7 - - - +
144D VAL* 1.3 74.1 - - - +
146D THR* 1.3 57.0 + - - +
148D LEU* 3.9 4.8 - - + +
149D ALA* 2.7 36.3 + - - +
190D LEU* 3.7 33.0 - - + +
191D LEU* 4.0 16.4 - - + -
194D TRP* 3.6 47.6 - - + +
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Residues in contact with THR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASN* 3.7 17.2 + - - +
142D ALA* 2.7 26.4 + - - +
143D VAL* 3.7 3.8 - - - -
145D LEU* 1.3 74.7 - - - +
147D GLN* 1.3 64.8 + - - +
149D ALA* 3.4 7.2 + - + +
150D ALA* 3.1 23.4 + - + +
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Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 3.9 33.4 + - - +
107D ASN* 3.5 29.1 + - - +
128D VAL* 3.2 16.8 - - + +
129D GLY 2.9 42.2 + - - +
143D VAL* 2.9 28.1 + - + +
144D VAL* 3.5 11.3 - - - +
146D THR* 1.3 78.3 - - - +
148D LEU* 1.3 61.0 + - - +
150D ALA* 3.4 9.4 + - - +
151D VAL* 3.5 17.3 + - - +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 5.6 0.4 - - + -
128D VAL* 4.4 12.1 - - + +
144D VAL 2.9 17.4 + - - +
145D LEU* 3.9 5.8 - - + +
147D GLN* 1.3 74.7 - - - +
149D ALA* 1.3 67.7 + - - +
151D VAL* 3.1 13.2 + - + +
152D ALA* 2.9 20.4 + - - +
160D TRP* 4.1 15.7 - - + -
165D ILE* 3.7 34.3 - - + -
191D LEU* 4.0 25.6 - - + +
194D TRP* 3.5 33.4 - - + -
195D VAL* 4.0 13.5 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU 2.7 22.5 + - - +
146D THR* 3.8 7.9 - - - +
147D GLN 3.3 0.2 - - - -
148D LEU* 1.3 73.6 - - - +
150D ALA* 1.3 62.3 + - - +
152D ALA* 3.3 1.2 + - - +
153D GLN* 3.0 42.0 + - + +
194D TRP* 3.8 26.2 - - + +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASN* 3.7 34.3 - - + +
108D GLU* 4.5 9.2 - - + +
111D ALA* 3.2 16.1 - - + +
146D THR* 3.1 17.9 + - + +
147D GLN 3.7 5.8 - - - +
148D LEU 3.2 0.2 - - - -
149D ALA* 1.3 76.8 - - - +
151D VAL* 1.3 63.9 + - - +
153D GLN* 3.5 22.0 + - - +
154D LYS* 3.8 5.0 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 5.4 2.0 - - - +
107D ASN 5.2 1.1 - - - +
110D VAL* 4.5 10.1 - - + -
111D ALA* 3.7 22.1 - - + +
114D VAL* 4.0 17.7 - - + -
126D VAL* 4.0 28.7 - - + -
128D VAL* 6.2 0.2 - - + -
147D GLN 3.7 13.0 - - - +
148D LEU* 3.1 12.1 + - + +
150D ALA* 1.3 74.9 - - - +
152D ALA* 1.3 65.9 - - - +
154D LYS* 3.0 14.7 + - - +
155D LEU* 3.5 31.9 + - + +
160D TRP* 5.1 7.6 - - + -
163D VAL* 5.8 1.1 - - + -
165D ILE* 6.0 0.2 - - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 3.4 6.3 + - - -
148D LEU 2.9 9.8 + - - +
149D ALA 3.6 3.4 - - - +
151D VAL* 1.3 76.8 - - - +
153D GLN* 1.3 64.0 + - + +
155D LEU* 3.0 24.1 + - - +
160D TRP* 4.1 22.9 + - + +
194D TRP* 3.5 35.2 - - + -
198D LYS* 6.0 0.7 - - + -
199D LEU* 5.5 2.5 - - + -
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 2.8 30.6 - - - +
149D ALA* 3.0 31.3 + - + +
150D ALA* 3.7 14.6 - - - +
151D VAL 3.2 0.2 - - - -
152D ALA* 1.3 77.5 - - + +
154D LYS* 1.3 66.1 + - + +
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 4.7 5.5 - - - +
108D GLU* 4.6 10.1 + - - +
111D ALA* 3.9 23.8 - - + +
112D ASP* 2.5 38.9 + - - +
115D ALA* 3.8 28.1 - - + +
150D ALA 3.9 3.4 - - - +
151D VAL 3.0 9.1 + - - +
153D GLN* 1.3 85.9 - - - +
155D LEU* 1.3 59.1 + - + +
156D SER 4.3 0.2 + - - -
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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
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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