Contacts of the helix formed by residues 158 - 174 (chain A) in PDB entry 3HXI
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 GLU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 4.5 12.3 - - - +
134A GLN* 4.1 12.6 - - - +
155A SER* 3.3 25.8 + - - +
157A ASN* 1.3 79.7 + - - +
159A GLU* 1.3 65.0 + - - +
160A GLU 3.3 2.2 - - - -
161A THR* 3.2 19.7 + - - +
162A ILE* 2.9 26.9 + - + +
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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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157A ASN 3.1 6.9 + - - +
158A GLU* 1.3 72.9 - - - +
160A GLU* 1.3 58.9 + - - +
162A ILE* 3.8 0.2 - - - +
163A LEU* 2.8 46.4 + - + +
201A TYR* 3.6 43.2 + - + +
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Residues in contact with GLU 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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158A GLU 3.3 0.8 - - - -
159A GLU* 1.3 80.8 - - - +
161A THR* 1.3 60.0 + - - +
163A LEU* 3.5 4.4 + - - +
164A SER* 3.0 27.9 + - - -
167A ARG* 4.3 5.5 + - - +
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Residues in contact with THR 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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130A GLU* 3.8 20.1 - - + +
131A GLU* 3.7 30.1 - - + +
134A GLN* 3.6 30.1 - - + -
158A GLU* 3.2 19.2 + - - +
160A GLU* 1.3 76.6 - - - +
162A ILE* 1.3 67.4 + - - +
164A SER* 3.0 8.8 + - - -
165A ILE* 3.0 25.1 + - + +
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Residues in contact with ILE 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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100A TRP* 2.9 39.9 + - + +
134A GLN* 4.5 4.3 - - - +
153A LEU* 3.8 19.1 - - + -
155A SER* 3.7 11.2 - - - +
156A ASP 3.6 30.7 - - - -
157A ASN 3.7 4.7 - - - +
158A GLU* 2.9 26.9 + - + +
159A GLU 3.8 3.1 - - - +
161A THR* 1.3 76.8 - - - +
163A LEU* 1.3 55.9 + - - +
165A ILE* 3.3 1.8 + - - +
166A GLY 3.0 12.0 + - - -
181A PHE* 3.6 32.1 - - + -
201A TYR* 3.8 20.4 - - + -
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Residues in contact with LEU 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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100A TRP* 4.3 5.6 - - + -
159A GLU* 2.8 38.5 + - + +
160A GLU* 3.9 4.5 - - - +
162A ILE* 1.3 71.6 - - + +
164A SER* 1.3 59.8 + - - +
166A GLY* 3.3 0.9 + - - -
167A ARG* 2.9 47.0 + - - +
201A TYR* 3.6 43.1 - - + -
202A GLU 4.7 0.2 - - - +
203A ILE* 3.2 39.7 - - + +
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Residues in contact with SER 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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131A GLU* 2.8 33.1 + - - +
160A GLU* 3.0 13.5 + - - -
161A THR* 3.0 13.9 + - - -
163A LEU* 1.3 75.1 - - - +
165A ILE* 1.3 56.1 + - - +
167A ARG* 3.4 28.7 + - - +
168A ARG* 3.0 28.8 + - - +
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Residues in contact with ILE 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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100A TRP* 4.0 10.1 - - + -
126A TRP* 3.7 29.1 - - + -
131A GLU* 3.4 42.8 - - + +
134A GLN* 3.7 19.1 - - + -
135A ILE* 4.0 8.7 - - + -
153A LEU* 4.0 18.4 - - + -
161A THR* 3.0 19.0 + - + +
162A ILE* 3.5 7.0 - - - +
164A SER* 1.3 73.8 - - - +
166A GLY* 1.3 67.7 + - - +
168A ARG* 3.3 2.8 + - - +
169A ILE* 2.9 36.3 + - + +
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Residues in contact with GLY 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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100A TRP* 3.4 32.6 - - - +
162A ILE 3.0 11.1 + - - -
163A LEU 3.3 2.2 + - - -
165A ILE* 1.3 74.9 - - - +
167A ARG* 1.3 62.6 + - - +
169A ILE* 3.3 2.9 + - - +
170A LYS* 3.1 27.2 + - - +
179A ILE* 3.5 8.0 - - - +
203A ILE* 3.8 8.3 - - - -
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Residues in contact with ARG 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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160A GLU* 4.3 6.1 + - - +
163A LEU* 2.9 27.1 + - - +
164A SER* 3.4 38.8 + - - +
166A GLY* 1.3 76.4 - - - +
168A ARG* 1.3 61.5 + - - +
170A LYS* 3.3 8.7 + - + +
171A GLU* 3.1 33.6 + - - +
203A ILE* 4.0 16.4 - - + -
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Residues in contact with ARG 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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120A LEU* 3.7 20.2 - - + -
125A ASP* 2.9 23.8 + - - -
126A TRP* 3.8 15.2 - - + -
127A ASP* 2.9 49.7 + - - +
131A GLU* 5.1 2.2 - - - +
164A SER 3.0 17.5 + - - +
165A ILE 3.7 4.3 - - - +
167A ARG* 1.3 74.7 - - - +
169A ILE* 1.3 63.5 + - - +
171A GLU* 3.2 20.9 + - - +
172A ARG* 3.0 61.0 + - - +
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Residues in contact with ILE 169 (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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100A TRP* 4.1 18.8 - - + -
102A ILE* 3.8 28.3 - - + -
117A LEU* 4.2 7.6 - - + -
120A LEU* 4.0 11.7 - - + -
126A TRP* 4.2 14.1 - - + -
151A VAL* 3.6 31.6 - - + -
165A ILE* 2.9 32.8 + - + +
166A GLY* 3.6 6.7 - - - +
168A ARG* 1.3 75.0 - - - +
170A LYS* 1.3 58.1 + - - +
172A ARG 3.3 0.3 + - - -
173A LEU* 2.9 40.6 + - + +
175A LEU* 4.4 5.2 - - + -
179A ILE* 4.8 4.0 - - + -
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Residues in contact with LYS 170 (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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166A GLY 3.1 15.0 + - - +
167A ARG* 3.3 8.5 + - + +
169A ILE* 1.3 75.0 - - - +
171A GLU* 1.3 57.8 + - + +
174A GLU* 2.9 25.1 + - - -
175A LEU* 3.0 41.4 + - + +
176A GLU 3.6 12.7 + - - -
177A ASP 3.2 27.7 + - - -
178A THR* 4.3 0.6 - - - +
179A ILE* 3.5 17.7 - - + -
203A ILE* 3.3 38.9 + - + +
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Residues in contact with GLU 171 (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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167A ARG* 3.1 25.0 + - - +
168A ARG* 3.2 35.2 + - - +
170A LYS* 1.3 77.3 - - + +
172A ARG* 1.3 75.3 + - - +
174A GLU* 3.2 18.8 + - - +
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Residues in contact with ARG 172 (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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112A PHE* 4.3 1.4 - - - -
116A GLU* 3.9 26.6 - - + +
120A LEU* 4.1 23.5 - - + +
125A ASP* 3.3 27.7 + - - +
168A ARG* 3.0 61.2 + - - +
169A ILE 4.1 0.2 - - - +
171A GLU* 1.3 92.1 + - - +
173A LEU* 1.3 71.4 - - + +
174A GLU* 3.3 7.2 + - - +
10C ARG* 5.0 19.5 - - - +
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Residues in contact with LEU 173 (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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102A ILE* 3.7 30.5 - - + -
108A GLN* 4.9 0.7 + - - -
112A PHE* 3.9 10.0 - - - -
113A LEU* 3.7 44.7 - - + +
116A GLU* 4.0 5.4 - - + -
117A LEU* 3.7 44.9 - - + +
120A LEU* 5.1 0.7 - - + -
149A LEU* 4.3 4.9 - - + -
169A ILE* 2.9 22.9 + - + +
172A ARG* 1.3 85.5 - - + +
174A GLU* 1.3 71.8 + - - +
175A LEU* 3.2 16.6 + - + +
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Residues in contact with GLU 174 (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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108A GLN* 4.9 4.0 + - - -
112A PHE* 4.0 22.5 - - + -
170A LYS 2.9 9.0 + - - -
171A GLU 3.2 13.3 + - - +
172A ARG 4.1 6.3 - - - +
173A LEU* 1.3 81.6 - - - +
175A LEU* 1.3 62.5 + - - +
176A GLU* 3.9 10.5 + - - +
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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