Contacts of the helix formed by residues 154 - 164 (chain B) in PDB entry 4XQ2
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 ASP 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU 4.5 2.4 + - - +
128B ILE* 6.0 1.8 - - + -
153B VAL* 1.3 71.2 - - - +
155B VAL* 1.3 63.7 + - - +
156B ALA* 3.3 10.6 + - - +
157B GLU* 3.1 33.0 + - + +
158B VAL* 3.0 26.7 + - + +
160B ARG* 5.7 0.3 + - - -
287B VAL* 3.8 29.1 - - + +
290B ALA* 6.5 0.7 - - - -
291B GLN* 3.7 8.0 - - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 4.6 11.4 - - + -
144B THR* 3.8 20.0 - - + -
153B VAL 3.0 9.1 + - - +
154B ASP* 1.3 70.9 - - - +
156B ALA* 1.3 52.9 + - - +
158B VAL* 3.7 0.9 - - - +
159B SER* 2.7 49.4 + - - +
171B VAL* 3.8 29.8 - - + -
181B GLN* 4.9 1.1 - - - +
183B PRO* 4.2 1.1 - - + +
186B LEU* 3.6 37.9 - - + -
188B ALA* 4.1 9.0 - - + +
291B GLN* 3.0 14.5 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP* 3.3 7.6 + - - +
155B VAL* 1.3 77.7 - - - +
157B GLU* 1.3 58.7 + - - +
159B SER* 3.3 1.8 + - - -
160B ARG* 2.8 48.8 + - - +
186B LEU* 3.2 34.3 + - + +
291B GLN* 4.7 0.8 + - - -
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 5.7 7.9 - - + +
128B ILE* 4.6 16.8 - - + +
154B ASP* 3.1 29.6 + - + +
156B ALA* 1.3 73.2 - - - +
158B VAL* 1.3 66.8 + - - +
160B ARG* 3.2 26.4 + - - +
161B ARG* 3.0 61.0 + - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.4 8.1 - - + +
128B ILE* 3.5 32.8 - - + -
132B LEU* 4.3 6.6 - - + +
140B VAL* 3.9 22.4 - - + -
142B ILE* 3.5 27.4 - - + -
153B VAL* 3.6 21.1 - - + -
154B ASP* 3.0 22.3 + - + +
155B VAL 3.9 0.2 - - - +
157B GLU* 1.3 74.8 - - - +
159B SER* 1.3 58.1 + - - +
161B ARG* 3.4 4.4 + - - +
162B ALA* 2.9 28.2 + - + +
169B VAL* 5.0 1.1 - - + -
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 2.7 28.7 + - - +
156B ALA 3.7 3.8 - - - -
158B VAL* 1.3 72.0 - - - +
160B ARG* 1.3 65.4 + - - +
163B HIS* 3.1 35.9 + - - -
169B VAL* 3.7 20.4 - - - +
187B GLY* 3.5 25.7 + - - -
188B ALA* 3.5 21.0 + - - -
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Residues in contact with ARG 160 (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 ASP* 5.7 0.2 + - - -
156B ALA* 2.8 35.5 + - - +
157B GLU* 3.2 40.8 + - - +
159B SER* 1.3 74.2 - - - +
161B ARG* 1.3 81.3 + - - +
163B HIS* 3.6 2.7 + - - +
164B GLU* 3.4 19.8 + - - +
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Residues in contact with ARG 161 (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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128B ILE* 4.2 13.0 - - + -
129B ALA* 5.4 7.9 - - + -
132B LEU* 3.5 24.1 - - + +
157B GLU* 3.0 51.3 + - - +
160B ARG* 1.3 97.9 + - - +
162B ALA* 1.3 61.5 + - - +
164B GLU* 3.2 44.9 + - - +
165B ARG* 3.6 9.5 - - - +
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Residues in contact with ALA 162 (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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132B LEU* 3.7 21.9 - - + +
140B VAL* 3.9 10.8 - - + -
158B VAL* 2.9 19.5 + - + +
159B SER 4.0 0.4 - - - +
160B ARG 3.3 0.2 - - - -
161B ARG* 1.3 75.0 - - - +
163B HIS* 1.3 55.5 + - - +
164B GLU 3.1 2.0 - - - -
165B ARG* 2.8 31.4 + - - +
166B GLY 3.5 2.3 + - - -
167B ALA* 3.6 10.7 + - + +
169B VAL* 3.5 27.8 - - + -
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Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B SER* 3.1 23.7 + - - +
160B ARG* 4.3 3.5 - - - +
162B ALA* 1.3 70.5 - - - +
164B GLU* 1.3 56.2 + - - +
165B ARG 2.9 5.8 - - - -
166B GLY* 2.8 25.1 + - - +
167B ALA 3.2 21.8 - - - +
169B VAL* 3.7 9.6 - - + +
187B GLY 2.9 29.1 + - - -
189B ASP* 2.6 34.9 + - - -
213B ARG* 5.7 0.9 - - - -
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Residues in contact with GLU 164 (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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160B ARG 3.4 9.4 + - - +
161B ARG* 3.2 54.6 + - - +
163B HIS* 1.3 77.2 - - - +
165B ARG* 1.3 58.1 + - + -
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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