Contacts of the helix formed by residues 170 - 185 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B SER 3.8 1.8 + - - -
169B LEU* 1.3 75.3 - - - +
171B LYS* 1.3 65.3 + - - +
172B GLU* 3.1 18.7 + - - +
173B GLN* 2.9 51.0 + - - +
174B LYS* 3.0 23.3 + - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ASN* 1.3 76.7 - - - +
172B GLU* 1.3 70.7 + - - +
174B LYS* 3.3 13.7 + - + +
175B ASP* 2.9 48.6 + - - +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ASN* 3.4 19.2 + - - +
171B LYS* 1.3 91.5 + - - +
173B GLN* 1.3 59.5 + - + +
175B ASP* 3.2 10.4 + - - +
176B LYS* 2.8 28.6 + - - +
179B ARG* 4.7 3.7 + - - +
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP 5.4 1.8 - - - +
49B ASP* 3.5 41.9 + - - +
51B GLY* 5.6 1.6 + - - -
168B SER 4.7 1.0 - - - +
169B LEU* 3.5 26.7 - - + +
170B ASN* 2.9 48.2 + - - +
172B GLU* 1.3 75.2 - - + +
174B LYS* 1.3 65.2 + - - +
176B LYS* 3.3 9.0 + - - +
177B LEU* 3.3 19.4 + - - +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 4.5 5.7 - - - +
166B TYR* 3.4 64.2 - - + +
167B ASN* 4.7 8.5 + - - +
169B LEU* 3.6 27.0 + - + +
170B ASN 3.0 18.2 + - - +
171B LYS* 3.3 15.0 + - + +
173B GLN* 1.3 75.2 - - - +
175B ASP* 1.3 66.9 + - - +
177B LEU* 3.3 19.2 - - - +
178B TYR* 3.3 6.9 + - - +
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS* 5.3 9.2 - - - -
171B LYS* 2.9 34.3 + - - +
172B GLU* 3.5 11.7 - - - +
174B LYS* 1.3 78.5 - - - +
176B LYS* 1.3 63.5 + - - +
178B TYR* 3.1 15.8 + - + +
179B ARG* 3.1 36.9 + - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP 5.6 2.0 - - - +
50B LYS* 2.8 38.8 + - - +
51B GLY* 4.4 1.1 - - - +
109B ARG* 4.6 6.0 - - - +
172B GLU 2.8 17.4 + - - +
173B GLN* 3.5 12.8 - - - +
174B LYS 3.3 0.2 - - - -
175B ASP* 1.3 71.8 - - - +
177B LEU* 1.3 59.2 + - - +
179B ARG* 3.1 33.5 + - - +
180B ASP* 2.9 56.9 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.6 40.2 - - + -
51B GLY* 4.1 5.6 - - - -
52B LEU* 3.7 29.2 - - + +
154B VAL* 4.1 6.5 - - + -
158B LEU* 4.0 25.6 - - + -
166B TYR* 3.9 30.3 - - + -
169B LEU* 4.8 5.2 - - + -
173B GLN 3.3 8.6 + - - +
174B LYS* 3.3 10.5 - - - +
176B LYS* 1.3 79.2 - - - +
178B TYR* 1.3 56.8 + - - +
180B ASP* 3.3 7.0 + - - +
181B VAL* 2.9 33.5 + - + +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ARG* 3.5 35.5 + - - +
150B ALA 4.0 3.6 - - - -
151B LYS* 3.8 41.5 - - + -
154B VAL* 3.6 20.7 - - + +
174B LYS 3.3 6.9 + - - +
175B ASP* 3.1 19.8 + - + +
177B LEU* 1.3 80.7 - - - +
179B ARG* 1.3 67.2 + - + +
181B VAL* 3.3 1.7 + - - +
182B GLU* 2.6 68.0 + - + +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLU 4.7 2.6 + - - -
175B ASP* 3.1 30.0 + - - +
176B LYS* 3.1 39.1 + - + +
178B TYR* 1.3 84.9 - - + +
180B ASP* 1.3 67.7 + - - +
182B GLU* 3.2 17.1 - - - +
183B GLU* 2.9 27.8 + - - +
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS 4.0 0.2 - - - +
51B GLY* 3.3 4.0 - - - -
52B LEU* 3.1 32.4 + - + +
109B ARG* 3.6 20.2 + - - +
176B LYS* 2.9 49.2 + - - -
177B LEU* 3.4 10.8 - - - +
179B ARG* 1.3 75.2 - - - +
181B VAL* 1.3 57.6 + - - +
183B GLU* 3.2 6.8 + - - +
184B ILE* 2.9 48.5 + - + +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.9 0.2 - - + -
52B LEU* 4.5 5.8 - - + -
145B LEU* 3.5 23.8 - - + +
150B ALA* 4.0 16.6 - - + +
153B ILE* 4.3 11.7 - - + -
154B VAL* 3.8 9.2 - - + -
158B LEU* 3.6 31.4 - - + -
177B LEU* 2.9 23.5 + - + +
178B TYR* 3.3 4.2 + - - +
180B ASP* 1.3 73.4 - - - +
182B GLU* 1.3 63.9 + - - +
185B PHE* 3.1 47.6 + - + +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B SER* 5.9 1.9 - - - -
145B LEU* 4.9 12.9 - - - +
147B ARG* 2.8 41.8 + - + +
150B ALA* 3.8 14.6 - - + +
178B TYR* 2.6 62.5 + - + +
179B ARG* 3.2 20.1 - - - +
181B VAL* 1.3 78.7 - - - +
183B GLU* 1.3 61.0 - - + +
185B PHE 4.3 8.7 - - - -
186B ASN* 5.6 0.7 - - - -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 5.1 0.5 + - - -
109B ARG* 3.3 26.0 + - - +
179B ARG 2.9 14.8 + - - +
180B ASP* 3.8 6.6 - - - +
182B GLU* 1.3 80.4 + - + +
184B ILE* 1.3 64.6 + - + +
186B ASN* 3.9 13.0 + - - -
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.6 7.6 - - + +
55B ILE* 4.0 35.7 - - + -
81B LYS* 2.8 37.0 + - + +
108B ILE* 4.3 10.5 - - + -
109B ARG* 3.7 43.5 - - + +
180B ASP* 2.9 30.2 + - + +
183B GLU* 1.3 79.6 - - + +
185B PHE* 1.3 84.7 + - + +
186B ASN* 3.2 2.3 + - - +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.5 45.1 - - + +
52B LEU* 3.5 32.8 - - + -
55B ILE* 3.6 33.0 - - + -
81B LYS* 3.8 15.0 - - + -
82B GLY* 3.7 9.6 - - - -
83B ILE* 3.9 7.9 - - + -
144B SER* 4.9 0.3 - - - -
145B LEU* 3.5 38.0 + - + +
158B LEU* 6.1 0.4 - - + -
181B VAL* 3.1 39.9 + - + +
182B GLU 4.3 5.1 - - - -
183B GLU 3.6 0.6 - - - -
184B ILE* 1.3 78.7 - - + +
186B ASN* 1.3 62.8 + - - +
187B TYR* 4.8 2.2 - - - -
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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