Contacts of the helix formed by residues 170 - 185 (chain A) in PDB entry 2X5Q
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER 3.7 1.6 + - - -
169A LEU* 1.3 75.7 - - - +
171A LYS* 1.3 60.0 + - - +
172A GLU* 3.1 16.4 + - - +
173A GLN* 2.8 50.1 + - - +
174A LYS* 3.0 29.9 + - - +
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Residues in contact with LYS 171 (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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170A ASN* 1.3 76.2 - - - +
172A GLU* 1.3 57.8 + - - +
174A LYS* 3.2 11.5 + - + +
175A ASP* 2.9 64.6 + - - +
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Residues in contact with GLU 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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170A ASN* 3.1 15.2 + - - +
171A LYS* 1.3 78.6 - - - +
173A GLN* 1.3 61.4 + - + +
175A ASP* 3.5 7.3 + - - +
176A LYS* 3.0 25.3 + - - +
179A ARG* 4.8 7.0 + - - +
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Residues in contact with GLN 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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48A ASP 5.5 0.7 - - - +
49A ASP* 3.6 43.9 + - + +
51A GLY* 5.7 1.0 - - - -
168A SER 4.5 1.4 - - - +
169A LEU* 3.4 27.6 - - + +
170A ASN* 2.8 52.8 + - - +
172A GLU* 1.3 73.5 - - + +
174A LYS* 1.3 65.5 + - - +
176A LYS* 3.1 17.1 + - - +
177A LEU* 3.1 13.5 + - - +
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Residues in contact with LYS 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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154A VAL* 4.8 4.2 - - - +
166A TYR* 3.6 59.2 + - + +
167A ASN* 4.8 7.4 + - - +
169A LEU* 2.9 34.7 + - + +
170A ASN* 3.0 17.9 + - - +
171A LYS* 3.2 12.0 + - + +
173A GLN* 1.3 75.6 - - - +
175A ASP* 1.3 63.7 + - - +
177A LEU* 3.3 7.3 + - - +
178A TYR* 3.1 21.1 + - - +
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Residues in contact with ASP 175 (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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171A LYS* 2.9 50.5 + - - +
172A GLU* 3.8 7.7 - - - +
174A LYS* 1.3 77.7 - - - +
176A LYS* 1.3 60.5 + - - +
178A TYR* 3.3 9.9 + - + +
179A ARG* 2.9 45.7 + - + +
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Residues in contact with LYS 176 (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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49A ASP 5.3 2.5 - - - +
50A LYS* 2.8 40.5 + - - +
51A GLY* 4.2 1.8 - - - -
109A ARG* 4.4 6.4 - - - +
172A GLU* 3.0 15.1 + - + +
173A GLN* 3.3 13.0 - - - +
175A ASP* 1.3 76.5 - - - +
177A LEU* 1.3 51.8 + - - +
179A ARG* 3.2 29.4 + - + +
180A ASP* 2.7 61.3 + - - +
183A GLU* 5.7 0.9 - - - -
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Residues in contact with LEU 177 (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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47A ILE* 3.8 32.1 - - + -
51A GLY* 4.4 4.7 - - - -
52A LEU* 3.8 32.3 - - + +
154A VAL* 4.0 11.0 - - + -
158A LEU* 3.9 24.9 - - + -
166A TYR* 3.8 32.5 - - + -
169A LEU* 4.9 4.7 - - + -
173A GLN 3.1 10.7 + - - +
174A LYS* 3.3 10.1 + - - +
176A LYS* 1.3 73.4 - - - +
178A TYR* 1.3 59.5 + - - +
180A ASP* 3.4 7.0 + - - +
181A VAL* 3.0 34.0 + - - +
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Residues in contact with TYR 178 (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 ARG* 3.1 50.7 + - - +
150A ALA* 3.4 28.3 - - + -
151A LYS* 3.6 25.8 - - + -
154A VAL* 3.8 15.8 - - + +
174A LYS 3.1 12.8 + - - +
175A ASP* 3.6 14.4 - - + +
176A LYS 3.3 0.2 - - - -
177A LEU* 1.3 73.6 - - - +
179A ARG* 1.3 76.5 + - + +
181A VAL* 3.2 1.6 + - - +
182A GLU* 3.0 31.7 + - + +
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Residues in contact with ARG 179 (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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172A GLU* 4.8 6.7 + - - +
175A ASP* 2.9 36.6 + - + +
176A LYS* 3.2 39.2 + - + +
178A TYR* 1.3 83.4 - - + +
180A ASP* 1.3 57.7 + - - +
182A GLU* 3.1 4.8 + - - +
183A GLU* 2.8 48.3 + - + +
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Residues in contact with ASP 180 (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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51A GLY* 3.2 2.3 - - - -
52A LEU* 2.8 38.5 + - + +
109A ARG* 3.5 16.0 + - - -
176A LYS* 2.7 53.0 + - - +
177A LEU* 3.4 10.5 - - - +
179A ARG* 1.3 71.2 - - - +
181A VAL* 1.3 57.6 + - - +
183A GLU* 3.2 11.2 + - - +
184A ILE* 2.9 46.5 + - + +
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Residues in contact with VAL 181 (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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52A LEU* 4.3 11.9 - - + -
145A LEU* 3.6 24.2 - - + +
150A ALA* 4.1 18.6 - - + +
153A ILE* 4.3 12.3 - - + -
154A VAL* 3.7 10.8 - - + -
158A LEU* 3.7 29.8 - - + -
177A LEU* 3.0 20.0 + - + +
178A TYR 3.7 4.3 - - - +
180A ASP* 1.3 75.5 - - - +
182A GLU* 1.3 62.7 - - - +
185A PHE* 3.3 37.7 + - + +
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Residues in contact with GLU 182 (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 SER* 4.9 5.4 + - - -
145A LEU* 2.7 45.3 + - - +
146A ASP 3.8 0.9 - - - +
147A ARG* 3.6 38.5 + - + +
150A ALA* 3.4 12.2 - - + +
178A TYR* 3.0 31.7 + - + +
179A ARG* 3.7 4.3 - - - +
181A VAL* 1.3 77.7 - - - +
183A GLU* 1.3 62.6 + - + +
185A PHE 4.4 2.4 + - - -
186A ASN* 4.5 8.0 - - - +
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Residues in contact with GLU 183 (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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81A LYS* 5.1 0.5 + - - -
109A ARG* 3.3 25.8 + - - +
176A LYS* 5.7 0.9 - - - -
179A ARG* 2.8 36.1 + - + +
180A ASP* 3.6 17.0 - - - +
182A GLU* 1.3 75.9 - - + +
184A ILE* 1.3 63.1 + - - +
186A ASN* 3.8 14.9 + - - -
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Residues in contact with ILE 184 (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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52A LEU* 4.7 8.1 - - + +
55A ILE* 3.8 35.7 - - + -
81A LYS* 2.6 47.6 + - + +
108A ILE* 4.2 10.3 - - + -
109A ARG* 3.7 39.3 - - + +
180A ASP* 2.9 33.9 + - + +
183A GLU* 1.3 75.3 - - - +
185A PHE* 1.3 74.7 + - + +
186A ASN* 2.9 8.4 + - - -
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Residues in contact with PHE 185 (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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15A ILE* 3.5 55.0 - - + +
52A LEU* 3.5 33.0 - - + -
55A ILE* 3.7 33.4 - - + -
81A LYS* 3.8 15.5 - - + -
82A GLY* 3.9 9.0 - - - -
83A ILE* 4.1 6.5 - - + -
145A LEU* 3.5 24.8 + - + +
158A LEU* 5.9 0.4 - - + -
181A VAL* 3.3 35.2 + - + +
182A GLU 4.4 1.5 + - - -
183A GLU 3.7 1.0 - - - -
184A ILE* 1.3 80.1 - - + +
186A ASN* 1.3 66.0 + - - +
187A TYR* 3.6 11.4 - - - -
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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