Contacts of the helix formed by residues 146 - 158 (chain A) in PDB entry 3RKQ
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU 3.9 1.6 + - - -
145A PHE* 1.3 75.1 - - - +
147A GLN* 1.3 67.8 + - - +
148A ALA* 3.6 8.5 + - - +
149A GLN* 2.9 40.0 + - - +
150A VAL* 2.9 21.7 + - - +
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Residues in contact with GLN 147 (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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145A PHE 3.9 0.4 + - - -
146A SER* 1.3 73.5 - - - +
148A ALA* 1.3 57.2 + - - +
150A VAL* 3.4 5.2 + - - +
151A TYR* 2.9 35.2 + - + +
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Residues in contact with ALA 148 (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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146A SER* 3.1 9.3 + - - +
147A GLN* 1.3 79.7 - - - +
149A GLN* 1.3 62.1 + - + +
151A TYR* 3.4 7.8 + - - +
152A GLU* 3.2 22.5 + - - +
175A LEU* 5.1 0.4 - - - +
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Residues in contact with GLN 149 (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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144A LEU 4.6 0.7 - - - +
145A PHE* 3.3 18.4 - - + +
146A SER* 2.9 48.1 + - - +
148A ALA* 1.3 73.6 - - + +
150A VAL* 1.3 61.6 + - - +
152A GLU* 3.2 4.5 + - - +
153A LEU* 2.9 33.1 + - + +
175A LEU* 2.7 50.3 + - + +
176A LYS* 4.3 5.7 + - - +
177A LEU* 3.7 24.5 - - + +
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Residues in contact with VAL 150 (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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145A PHE* 3.8 28.3 - - + +
146A SER 2.9 19.1 + - - +
147A GLN* 3.9 6.1 - - - +
149A GLN* 1.3 74.2 - - - +
151A TYR* 1.3 57.7 + - - +
153A LEU* 3.6 8.2 - - + +
154A GLU* 2.8 47.2 + - + +
185A TRP* 4.7 9.6 - - + +
3C A 4.8 9.0 - - - +
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Residues in contact with TYR 151 (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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147A GLN* 2.9 21.7 + - + +
148A ALA* 3.5 8.5 - - - +
149A GLN 3.2 0.2 - - - -
150A VAL* 1.3 78.8 - - - +
152A GLU* 1.3 61.0 + - - +
154A GLU* 3.8 6.5 - - + +
155A ARG* 3.0 38.9 + - + +
158A LYS* 6.3 1.1 - - - -
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Residues in contact with GLU 152 (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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148A ALA 3.2 9.3 + - - +
149A GLN 3.6 2.2 - - - +
151A TYR* 1.3 78.7 - - - +
153A LEU* 1.3 64.0 + - - +
155A ARG* 3.0 44.0 + - - +
156A ARG* 3.1 40.7 + - - +
171A LEU* 4.1 11.7 - - + +
174A VAL* 5.1 7.0 - - + +
175A LEU* 3.5 33.0 - - + -
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Residues in contact with LEU 153 (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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145A PHE* 4.2 14.8 - - + -
149A GLN 2.9 25.6 + - - +
150A VAL* 3.3 7.2 + - - +
152A GLU* 1.3 77.6 - - - +
154A GLU* 1.3 57.5 + - - +
156A ARG* 3.3 7.2 + - - +
157A PHE* 2.9 28.4 + - - +
171A LEU* 4.1 7.9 - - + -
175A LEU* 3.7 22.9 - - + -
177A LEU* 4.7 5.6 - - + -
182A VAL* 4.7 9.2 - - + -
185A TRP* 3.6 60.4 - - + +
186A PHE* 4.0 16.2 - - + -
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Residues in contact with GLU 154 (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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150A VAL* 2.8 36.4 + - + +
151A TYR* 3.8 7.0 - - + +
153A LEU* 1.3 74.0 - - - +
155A ARG* 1.3 65.2 + - - +
157A PHE* 3.8 5.1 - - - +
158A LYS* 3.2 40.4 + - - +
185A TRP* 4.0 12.0 - - + -
189A ARG* 2.9 41.7 + - - -
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Residues in contact with ARG 155 (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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151A TYR* 3.0 30.0 + - + +
152A GLU* 3.0 42.1 + - - +
153A LEU 3.2 0.2 - - - -
154A GLU* 1.3 78.0 - - - +
156A ARG* 1.3 74.5 + - - +
158A LYS* 3.3 22.4 + - + +
159A GLN* 3.6 36.7 + - + +
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Residues in contact with ARG 156 (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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152A GLU* 3.1 35.1 + - - +
153A LEU 3.8 3.6 - - - +
155A ARG* 1.3 85.4 - - - +
157A PHE* 1.3 51.8 + - - +
159A GLN* 2.8 34.9 + - - +
160A GLN* 2.8 61.6 + - - +
163A LEU* 3.8 16.3 - - - +
167A GLU* 4.4 16.8 + - - +
171A LEU* 3.9 26.7 - - + +
186A PHE* 4.1 13.7 - - + -
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Residues in contact with PHE 157 (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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153A LEU 2.9 16.6 + - - +
154A GLU* 3.8 9.6 - - - +
155A ARG 3.2 0.4 - - - -
156A ARG* 1.3 76.6 - - - +
158A LYS* 1.3 63.8 + - + +
159A GLN 3.1 0.7 + - - -
160A GLN 3.3 17.4 + - - +
161A ARG* 3.6 54.6 + - + +
185A TRP* 4.1 6.5 - + + -
186A PHE* 3.9 23.3 - + + -
189A ARG* 3.6 61.0 - - + -
190A ARG* 4.1 15.7 - - + -
193A SER* 4.6 1.6 - - - -
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Residues in contact with LYS 158 (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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151A TYR* 6.3 1.0 - - - -
154A GLU* 3.2 29.0 - - - +
155A ARG* 3.3 13.2 + - + +
156A ARG 3.2 0.6 - - - -
157A PHE* 1.3 80.1 - - + +
159A GLN* 1.3 61.2 + - + +
189A ARG* 6.4 0.7 - - - +
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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