Contacts of the helix formed by residues 142 - 159 (chain A) in PDB entry 2HQQ
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 ASN 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ASP* 3.5 32.2 - - + +
120A VAL 2.9 27.3 + - - +
121A SER* 4.7 0.4 - - - +
141A ARG* 1.3 74.6 - - - +
143A ALA* 1.3 63.4 + - - +
144A SER* 3.3 3.6 - - - +
145A GLU* 3.3 26.6 + - + +
146A GLN* 3.0 34.5 + - - +
149A MET* 5.0 0.2 - - - +
178A GLU* 4.0 6.1 - - - -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG 3.4 2.8 + - - -
142A ASN* 1.3 74.5 - - - +
144A SER* 1.3 54.5 + - - +
146A GLN* 3.6 11.1 - - - +
147A VAL* 2.7 38.7 + - - +
178A GLU* 3.1 41.7 + - + +
179A LEU* 4.1 13.9 - - + -
181A GLN* 3.7 12.3 - - + +
182A LEU* 4.2 7.4 - - + -
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.3 1.6 + - - +
143A ALA* 1.3 77.8 - - - +
145A GLU* 1.3 73.3 + - - +
147A VAL* 3.6 9.7 + - - +
148A LYS* 3.6 21.5 + - - +
178A GLU* 5.0 1.4 + - - -
181A GLN* 4.3 14.0 - - - +
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Residues in contact with GLU 145 (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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120A VAL 4.5 1.3 - - - +
121A SER* 3.7 11.4 - - - -
122A ALA* 2.7 42.7 + - - +
123A THR 4.4 0.5 + - - -
142A ASN* 3.3 31.1 + - + +
143A ALA 3.3 0.2 - - - -
144A SER* 1.3 86.1 + - - +
146A GLN* 1.3 66.1 + - - +
148A LYS* 2.9 35.2 + - - +
149A MET* 3.2 22.4 + - + +
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Residues in contact with GLN 146 (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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9A VAL* 5.1 8.1 + - - +
10A GLY* 5.9 0.8 - - - -
138A ILE* 3.4 26.6 - - + +
139A GLU 2.9 23.0 + - - +
140A GLY* 3.4 6.4 - - - -
141A ARG* 2.8 25.0 + - - +
142A ASN* 3.0 39.1 + - - +
143A ALA* 3.1 4.2 + - - +
145A GLU* 1.3 77.0 - - - +
147A VAL* 1.3 58.6 + - - +
149A MET* 3.1 23.4 + - + +
150A LEU* 2.8 33.0 + - + +
182A LEU* 3.8 13.7 - - + +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA 2.7 23.8 + - - +
144A SER* 3.8 7.0 - - - +
145A GLU 3.2 0.2 - - - -
146A GLN* 1.3 73.2 - - - +
148A LYS* 1.3 52.5 + - + +
150A LEU* 3.1 9.7 + - - +
151A GLN* 2.7 52.7 + - - +
181A GLN* 3.6 25.6 - - + +
182A LEU* 3.9 17.7 - - + -
185A TYR* 3.3 37.2 - - + +
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Residues in contact with LYS 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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122A ALA* 3.7 19.4 - - + +
144A SER* 3.6 16.6 + - - +
145A GLU* 2.9 37.1 + - - +
147A VAL* 1.3 75.7 - - + +
149A MET* 1.3 66.1 + - - +
151A GLN* 3.2 18.2 + - - +
152A ARG* 2.9 23.7 + - - +
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Residues in contact with MET 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.5 14.4 - - + -
120A VAL* 3.4 34.8 - - + +
121A SER* 3.7 18.8 - - - +
122A ALA* 4.0 6.5 - - - +
125A PHE* 3.6 45.7 - - + -
138A ILE* 4.4 12.6 - - + -
142A ASN* 5.0 0.2 - - - +
145A GLU* 3.5 9.4 - - + +
146A GLN* 3.1 34.7 + - + +
148A LYS* 1.3 77.6 - - - +
150A LEU* 1.3 58.6 + - - +
152A ARG* 3.2 6.7 + - - +
153A ILE* 3.0 31.2 + - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.6 23.8 - - + -
146A GLN* 2.8 21.7 + - + +
147A VAL* 3.5 6.7 - - - +
149A MET* 1.3 75.9 - - - +
151A GLN* 1.3 57.3 + - - +
153A ILE* 3.3 9.4 + - + +
154A ASP* 3.0 34.6 + - - +
168A VAL* 3.5 32.5 - - + -
170A VAL* 4.0 13.2 - - + -
182A LEU* 3.8 24.7 - - + -
185A TYR* 3.7 36.1 - - + -
186A GLY 4.9 0.4 - - - +
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Residues in contact with GLN 151 (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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147A VAL* 2.7 30.6 + - - +
148A LYS* 3.6 21.7 + - - +
150A LEU* 1.3 69.3 - - - +
152A ARG* 1.3 60.4 + - - +
154A ASP* 3.3 9.4 + - - +
155A ALA* 2.9 31.4 + - - +
185A TYR* 3.3 28.7 + - + -
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Residues in contact with ARG 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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125A PHE* 3.0 33.0 + - + -
126A GLU* 3.4 32.8 + - - +
128A VAL* 2.9 29.5 + - - +
130A LEU* 3.5 32.8 - - + +
148A LYS 2.9 13.2 + - - +
149A MET* 3.4 11.0 - - - +
151A GLN* 1.3 78.6 - - - +
153A ILE* 1.3 62.7 + - - +
155A ALA* 3.5 6.2 + - + +
156A HIS* 3.0 22.7 + - - +
159A ARG* 5.1 0.7 + - - -
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Residues in contact with ILE 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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125A PHE* 3.8 23.1 - - + -
130A LEU* 4.3 5.4 - - + -
136A ILE* 3.8 35.0 - - + -
138A ILE* 4.7 2.5 - - + -
149A MET 3.0 15.6 + - - +
150A LEU* 3.7 20.0 - - + +
151A GLN 3.3 0.2 - - - -
152A ARG* 1.3 76.4 - - - +
154A ASP* 1.3 58.3 + - - +
156A HIS* 3.2 7.6 + - - +
157A ASN* 2.9 38.5 + - - +
166A ILE* 4.3 18.2 - - + -
168A VAL* 3.7 28.9 - - + -
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Residues in contact with ASP 154 (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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150A LEU* 3.0 18.6 + - - +
151A GLN* 3.5 11.3 - - - +
153A ILE* 1.3 75.7 - - - +
155A ALA* 1.3 65.5 + - - +
157A ASN* 3.0 21.0 + - - +
158A THR* 3.0 21.5 + - + +
168A VAL* 5.6 3.3 - - - +
185A TYR* 3.9 15.0 - - - -
216A ARG* 2.9 45.4 + - - -
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Residues in contact with ALA 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 GLN 2.9 20.3 + - - +
152A ARG* 3.8 7.0 - - + +
154A ASP* 1.3 72.4 - - - +
156A HIS* 1.3 62.7 + - - +
158A THR* 2.7 28.8 + - - -
159A ARG* 3.5 21.8 + - - +
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Residues in contact with HIS 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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130A LEU* 3.7 34.5 + - + +
131A THR* 4.3 21.6 - - + -
152A ARG 3.0 14.9 + - - +
153A ILE 3.3 8.1 - - - +
154A ASP 3.2 0.2 - - - -
155A ALA* 1.3 77.4 - - - +
157A ASN* 1.3 77.7 + - - +
159A ARG* 3.2 32.3 + - - +
160A GLN* 3.2 46.9 + - + +
164A GLN 4.9 1.6 + - - -
166A ILE* 3.7 22.9 - - + +
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Residues in contact with ASN 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 ILE* 2.9 27.7 + - - +
154A ASP* 3.0 11.7 + - - +
156A HIS* 1.3 85.4 - - - +
158A THR* 1.3 60.9 + - + +
160A GLN* 3.0 13.8 + - - +
164A GLN 4.5 0.2 - - - +
165A LYS* 2.7 46.7 + - + +
166A ILE* 2.8 46.7 + - - +
168A VAL* 4.9 2.4 - - - +
187A ASP* 5.6 0.6 + - - -
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Residues in contact with THR 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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154A ASP* 3.0 20.1 + - + +
155A ALA* 2.7 22.4 + - - +
157A ASN* 1.3 77.0 - - + +
159A ARG* 1.3 64.9 + - - +
160A GLN 3.3 7.1 + - - +
165A LYS* 4.3 5.3 + - - +
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Residues in contact with ARG 159 (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 ARG 5.1 0.8 + - - -
155A ALA* 3.5 18.7 + - - +
156A HIS* 3.2 39.3 + - - +
157A ASN 3.1 0.8 - - - -
158A THR* 1.3 82.9 + - - +
160A GLN* 1.3 73.0 + - - +
161A PRO* 4.3 2.9 - - - +
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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