Contacts of the helix formed by residues 169 - 182 (chain B) in PDB entry 1XB4
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 PRO 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B TRP* 3.6 28.7 - - + -
45B TYR* 4.1 26.9 - - + +
156B GLU* 6.1 0.2 - - - +
167B ARG 3.5 3.1 - - - +
168B MET* 1.3 94.7 - - + +
170B GLU* 1.3 62.0 + - - +
171B SER* 4.2 7.4 - - - +
172B LEU* 4.1 19.1 - - + -
173B LEU* 2.9 24.3 + - - +
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Residues in contact with GLU 170 (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 LEU* 3.7 28.6 + - + +
152B TYR* 2.9 53.8 + - - +
155B SER* 5.0 3.6 - - - -
156B GLU* 5.6 1.7 - - - +
168B MET 4.3 2.2 - - - +
169B PRO* 1.3 71.3 - - - +
171B SER* 1.3 56.8 + - - +
173B LEU* 2.8 9.5 + - - +
174B TYR* 2.7 35.2 + - - +
195B LYS* 5.0 12.5 + - - -
196B VAL 4.9 4.3 - - - +
197B ILE* 5.0 5.5 - - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 3.6 20.1 + - - -
109B SER 5.3 10.0 + - - -
110B GLY* 6.2 1.3 - - - -
169B PRO* 4.2 2.8 - - - +
170B GLU* 1.3 79.3 - - - +
172B LEU* 1.3 72.3 + - - +
174B TYR* 3.4 12.6 - - - +
175B TYR* 3.1 25.7 - - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.2 15.9 - - + -
45B TYR* 4.0 18.6 - - + +
106B ILE* 4.0 21.5 - - + -
109B SER 6.0 0.7 - - - +
122B PHE* 3.2 66.5 - - + -
168B MET* 4.0 5.2 - - + -
169B PRO* 3.5 16.9 + - + +
170B GLU 3.1 0.4 - - - -
171B SER* 1.3 93.3 + - - +
173B LEU* 1.3 66.1 + - - +
174B TYR 3.2 0.4 - - - -
175B TYR* 3.2 18.2 + - + +
176B CYS* 3.3 16.3 + - - -
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Residues in contact with LEU 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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135B ILE* 3.4 32.1 - - + -
151B LEU* 3.5 30.7 - - + +
154B LEU* 3.7 20.0 - - + +
155B SER* 4.1 8.1 - - - +
165B PHE* 5.1 6.5 - - + +
168B MET* 3.5 33.2 - - + +
169B PRO 2.9 16.0 + - - +
170B GLU* 2.8 8.9 + - - +
172B LEU* 1.3 79.0 - - - +
174B TYR* 1.3 62.0 - - - +
176B CYS* 2.8 15.6 + - - +
177B LEU* 3.1 28.4 + - + +
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Residues in contact with TYR 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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151B LEU* 4.4 9.4 - - + +
170B GLU 2.7 10.7 + - - +
171B SER* 3.4 13.2 - - - +
173B LEU* 1.3 76.5 - - - +
175B TYR* 1.3 96.7 + + - +
177B LEU* 3.1 11.0 + - - +
178B LYS* 3.0 48.1 + - + +
188B MET* 3.4 35.5 - - + +
196B VAL* 3.7 24.9 - - + -
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Residues in contact with TYR 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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104B LEU* 4.0 20.4 - - + -
106B ILE* 5.3 1.1 - - + -
110B GLY* 3.3 13.1 - - - -
111B ARG* 2.6 68.1 + - + +
122B PHE* 4.8 0.4 - - + -
128B LEU* 4.2 19.1 - - + +
171B SER* 3.1 31.0 - - - -
172B LEU* 3.2 17.5 + - + +
173B LEU 3.2 0.6 - - - -
174B TYR* 1.3 100.4 - + - +
176B CYS* 1.3 58.1 + - - +
178B LYS* 3.7 9.5 - - + +
179B PRO* 3.2 19.9 - - - +
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Residues in contact with CYS 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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122B PHE* 4.0 3.1 - - - -
128B LEU* 3.8 23.3 - - - +
131B TRP* 3.7 25.8 - - + -
132B ALA* 3.3 22.4 - - - +
135B ILE* 4.0 12.8 - - + -
168B MET* 3.6 27.6 - - - -
172B LEU 3.3 16.8 - - - -
173B LEU 2.8 7.8 + - - +
175B TYR* 1.3 77.4 - - - +
177B LEU* 1.3 61.5 + - - +
179B PRO* 3.0 12.6 - - - +
180B LEU* 4.9 0.2 - - - +
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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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135B ILE* 4.0 26.0 - - + -
139B PHE* 4.9 2.2 - - + -
151B LEU* 3.3 34.5 - - + -
154B LEU* 3.9 13.7 - - + -
173B LEU* 3.1 21.9 + - + +
174B TYR* 3.1 6.7 + - - +
176B CYS* 1.3 75.4 - - - +
178B LYS* 1.3 55.8 + - - +
179B PRO* 3.0 3.4 - - - -
180B LEU* 2.4 56.7 + - + +
181B CYS* 3.3 3.8 + - - -
188B MET* 5.1 5.6 - - - -
199B ILE* 3.7 30.1 - - + -
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Residues in contact with LYS 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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174B TYR* 3.0 40.5 + - + +
175B TYR* 3.7 15.3 - - + +
177B LEU* 1.3 74.6 - - - +
179B PRO* 1.3 59.6 - - + +
181B CYS* 2.6 37.9 + - + +
182B ASP* 3.0 34.9 + - - +
188B MET* 3.9 16.8 - - + -
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Residues in contact with PRO 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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128B LEU* 4.7 8.5 - - + +
129B ASP* 3.7 22.9 - - - +
132B ALA* 3.7 19.7 - - + -
175B TYR 3.2 15.3 - - - +
176B CYS* 3.0 19.7 - - - +
178B LYS* 1.3 91.6 - - + +
180B LEU* 1.3 52.7 + - + +
182B ASP* 2.3 41.3 - - + +
183B ARG* 3.5 16.5 - - - -
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Residues in contact with LEU 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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132B ALA* 3.8 38.4 - - + +
133B SER* 5.6 0.2 - - - -
135B ILE* 5.2 1.1 - - + -
136B LEU* 4.3 24.7 - - + +
139B PHE* 5.5 0.2 - - + -
177B LEU* 2.4 50.5 + - + +
179B PRO* 1.3 71.4 - - - +
181B CYS* 1.3 52.5 + - - -
182B ASP 2.6 16.0 - - - +
183B ARG* 4.2 17.3 - - - +
185B ARG* 2.8 34.0 + - + -
186B ALA* 3.0 18.9 + - + -
201B VAL* 4.0 17.9 - - + -
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Residues in contact with CYS 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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177B LEU 3.3 5.8 + - - -
178B LYS* 2.6 23.6 + - - +
180B LEU* 1.3 68.9 - - - +
182B ASP* 1.3 66.5 + - - +
184B ASN* 3.3 17.2 + - - +
186B ALA* 3.5 26.5 - - - +
187B THR* 4.8 0.2 - - - -
188B MET* 3.4 50.9 - - + -
199B ILE* 5.0 0.4 - - - -
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Residues in contact with ASP 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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178B LYS* 3.4 36.7 + - - +
179B PRO* 2.3 33.1 - - + +
180B LEU 2.6 11.3 - - - +
181B CYS* 1.3 77.7 - - - +
183B ARG* 1.3 64.8 + - + +
184B ASN* 2.9 2.2 - - - -
152C TYR* 5.8 0.5 + - - -
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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