Contacts of the helix formed by residues 152 - 168 (chain A) in PDB entry 2H4Q
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 ALA 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ASN* 3.0 30.3 + - + +
151A THR* 1.3 80.8 - - - +
153A PRO* 1.3 68.1 - - - +
154A GLU 3.3 2.6 + - - -
155A GLN* 3.5 22.8 + - + +
156A SER* 2.8 24.9 + - - +
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Residues in contact with PRO 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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149A PHE* 3.4 17.5 - - - +
150A LYS 4.6 1.1 - - - +
151A THR* 3.8 4.3 - - - -
152A ALA* 1.3 88.9 - - - +
154A GLU* 1.3 57.3 - - + +
156A SER* 3.2 5.2 + - - -
157A ARG* 2.7 36.5 + - - +
181A VAL* 3.6 22.3 - - + +
182A LYS* 4.0 15.9 - - - +
183A ALA* 3.8 16.4 - - - +
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Residues in contact with GLU 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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152A ALA 3.3 0.6 - - - -
153A PRO* 1.3 81.9 - - + +
155A GLN* 1.3 60.9 + - - +
157A ARG* 3.2 38.1 + - - +
158A LYS* 3.0 30.7 + - - +
178A SER* 3.5 31.0 - - - +
181A VAL 5.2 2.8 - - - +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ALA* 3.5 23.9 + - + +
154A GLU* 1.3 78.2 - - - +
156A SER* 1.3 62.3 + - - +
158A LYS* 3.9 5.3 - - - +
159A GLU* 3.2 25.1 + - + +
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Residues in contact with SER 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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147A VAL* 3.7 9.0 - - - +
148A ASN* 3.0 27.2 + - - +
149A PHE* 3.8 26.5 - - - -
152A ALA* 2.8 22.2 + - - +
153A PRO 3.5 4.0 - - - -
155A GLN* 1.3 75.4 - - - +
157A ARG* 1.3 64.2 + - - +
159A GLU* 3.1 23.6 - - - +
160A ILE* 3.2 16.7 - - - +
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Residues in contact with ARG 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 PRO 2.7 20.2 + - - +
154A GLU* 3.2 33.5 + - - +
156A SER* 1.3 72.7 - - - +
158A LYS* 1.3 65.5 + - - +
160A ILE* 3.4 7.1 + - - +
161A ASN* 3.0 40.9 + - - +
174A ASN* 5.7 4.4 - - - +
176A LEU* 3.4 26.3 + - + +
177A SER* 3.3 20.2 - - - +
178A SER* 3.2 28.2 - - - +
181A VAL* 3.7 30.2 - - + +
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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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154A GLU 3.0 17.9 + - - +
155A GLN* 3.9 6.3 - - - +
156A SER 3.3 0.2 - - - -
157A ARG* 1.3 87.5 - - - +
159A GLU* 1.3 53.3 + - - +
161A ASN* 3.4 7.4 + - - +
162A THR* 2.8 38.1 + - - +
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Residues in contact with GLU 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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121A TYR* 4.2 2.7 + - + -
145A GLN* 4.2 22.4 - - - +
147A VAL* 4.4 9.6 - - + -
155A GLN* 3.2 14.1 + - + +
156A SER* 3.1 21.5 - - - +
158A LYS* 1.3 76.2 - - - +
160A ILE* 1.3 67.2 + - + +
162A THR* 3.5 7.4 + - - -
163A TRP* 3.1 22.0 + - - +
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Residues in contact with ILE 160 (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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121A TYR* 3.6 55.6 - - + -
147A VAL* 5.5 0.2 - - + -
149A PHE* 4.3 7.0 - - + -
156A SER* 3.2 21.0 + - - +
157A ARG* 3.6 6.7 - - - +
158A LYS 3.3 0.2 - - - -
159A GLU* 1.3 75.5 - - + +
161A ASN* 1.3 60.6 + - - +
163A TRP* 3.1 5.0 + - - +
164A VAL* 3.0 34.1 + - + +
175A LEU* 5.5 0.7 - - + -
176A LEU* 3.7 21.5 - - + -
188A ILE* 3.7 28.9 - - + -
190A VAL* 4.2 14.1 - - + -
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Residues in contact with ASN 161 (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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157A ARG* 3.0 31.2 + - - +
158A LYS* 3.7 7.1 - - - +
160A ILE* 1.3 77.1 - - - +
162A THR* 1.3 57.0 + - - +
164A VAL* 3.8 5.9 - - - +
165A GLU* 2.9 29.2 + - - +
172A ILE 4.2 1.0 - - - +
173A LYS 3.5 16.7 - - - +
174A ASN* 3.7 15.7 - - - +
175A LEU* 3.3 12.3 + - - +
176A LEU* 2.8 55.1 + - - +
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Residues in contact with THR 162 (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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158A LYS* 2.8 22.6 + - - +
159A GLU* 3.6 9.5 - - - -
160A ILE 3.2 0.2 - - - -
161A ASN* 1.3 75.1 - - - +
163A TRP* 1.3 64.7 + - - +
165A GLU* 3.4 17.6 + - - +
166A LYS* 3.0 21.8 + - + +
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Residues in contact with TRP 163 (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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117A ALA* 3.8 32.3 - - + -
118A ASN 3.9 6.5 - - - -
119A ARG* 3.7 44.8 - - + +
121A TYR* 3.1 29.4 - + - +
159A GLU 3.1 9.0 + - - +
160A ILE 3.1 5.2 + - - +
162A THR* 1.3 74.2 - - - +
164A VAL* 1.3 79.4 + - + +
166A LYS* 3.0 9.5 + - + +
167A GLN* 2.9 69.1 + - + +
190A VAL* 3.8 25.6 - - + -
192A ALA* 4.5 5.4 - - + -
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Residues in contact with VAL 164 (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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160A ILE* 3.0 23.9 + - + +
161A ASN* 3.8 6.5 - - - +
163A TRP* 1.3 84.8 - - + +
165A GLU* 1.3 55.1 - - - +
167A GLN* 3.3 4.4 + - - -
168A THR* 2.7 37.8 + - + +
172A ILE* 3.7 26.0 - - + +
175A LEU* 3.8 17.5 - - + -
190A VAL* 3.8 29.6 - - + -
192A ALA* 5.2 1.1 - - + -
363A ALA* 3.7 24.0 - - + -
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Residues in contact with GLU 165 (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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161A ASN 2.9 17.8 + - - +
162A THR* 3.4 20.5 + - - +
164A VAL* 1.3 76.5 - - - +
166A LYS* 1.3 61.0 + - - +
168A THR* 3.3 4.6 + - - -
169A GLU 3.3 0.2 + - - -
170A SER* 2.7 52.2 + - - +
172A ILE 3.4 12.9 + - - +
173A LYS* 3.7 41.1 - - + +
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Residues in contact with LYS 166 (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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115A ARG* 4.2 10.9 - - - -
162A THR* 3.0 13.1 + - + +
163A TRP* 3.0 12.9 + - + +
165A GLU* 1.3 78.7 - - - +
167A GLN* 1.3 71.2 + - - +
168A THR 3.4 0.3 + - - -
169A GLU* 3.6 10.4 + - - +
170A SER* 5.1 0.7 - - - +
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Residues in contact with GLN 167 (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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115A ARG* 3.5 23.0 + - - +
117A ALA* 3.8 18.3 - - + +
163A TRP* 2.9 74.0 + - + +
164A VAL 3.3 2.6 + - - +
166A LYS* 1.3 85.4 - - - +
168A THR* 1.3 58.1 + - - +
169A GLU 3.4 0.7 - - - -
192A ALA* 3.5 21.3 - - + -
193A ILE 4.9 0.7 - - - -
194A TYR* 3.4 21.7 + - - +
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Residues in contact with THR 168 (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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164A VAL* 2.7 29.8 + - + +
165A GLU 3.3 5.9 + - - -
166A LYS 3.2 0.4 - - - -
167A GLN* 1.3 78.3 - - - +
169A GLU* 1.3 69.1 + - - +
171A LYS* 3.2 17.0 + - - +
172A ILE* 3.2 42.9 + - + +
192A ALA* 4.4 6.7 - - + -
193A ILE 4.6 0.2 - - - +
194A TYR* 3.6 7.7 - - - -
361A VAL* 3.3 27.1 - - + +
362A ALA 4.1 12.8 - - - +
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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