Contacts of the helix formed by residues 181 - 191 (chain B) in PDB entry 2XFN
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 SER 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ASP* 2.6 32.1 + - - -
146B MET 3.6 6.7 - - - -
148B MET 4.4 0.7 - - - -
180B VAL* 1.3 73.5 - - - +
182B ALA* 1.3 61.3 + - - +
183B LEU 3.1 5.7 + - - -
184B TRP* 3.0 20.6 + - - +
185B PHE* 3.0 24.1 + - - +
402B PHE* 2.8 20.9 + - - -
403B PRO 3.8 11.8 - - - -
404B PRO* 4.0 7.9 - - - -
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Residues in contact with ALA 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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143B TRP* 3.4 12.6 - - + +
146B MET* 2.9 30.1 + - + +
147B THR 3.9 6.1 - - - +
148B MET* 3.8 24.2 - - - +
151B LEU* 4.1 14.4 - - + -
180B VAL 3.6 1.6 + - - -
181B SER* 1.3 68.7 - - - +
183B LEU* 1.3 67.6 + - - +
185B PHE* 3.8 0.3 - - - +
186B LEU* 2.9 33.6 + - + +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 4.0 21.8 - - + -
134B PRO* 3.8 27.6 - - + +
137B ALA* 4.1 11.7 - - + -
140B ALA* 3.6 21.1 - - + +
143B TRP* 3.1 21.9 + - + +
144B ASP* 3.5 20.4 - - + +
181B SER* 3.1 5.6 + - - +
182B ALA* 1.3 75.5 - - - +
184B TRP* 1.3 57.9 + - - +
186B LEU* 3.8 4.0 - - - +
187B TRP* 2.9 28.4 + - - +
407B LEU* 3.9 20.2 - - + -
408B THR* 3.7 20.4 - - + -
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Residues in contact with TRP 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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173B VAL* 3.4 33.9 - - + -
180B VAL* 3.8 27.1 - - + -
181B SER* 3.0 15.7 + - - -
183B LEU* 1.3 77.4 - - - +
185B PHE* 1.3 75.9 + - - +
187B TRP* 3.3 30.9 + + - +
188B TYR* 2.8 47.6 + + - +
399B THR* 4.9 1.1 - - + -
400B THR 3.3 21.1 + - - -
401B TYR* 3.4 22.4 - - + -
402B PHE* 3.4 53.3 - + + -
407B LEU* 3.6 20.1 - - + +
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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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122B MET* 3.3 29.2 - - + -
148B MET* 3.5 40.8 - - + -
168B PHE* 3.6 18.6 - + - -
169B VAL* 3.8 30.1 - - + -
172B CYS* 3.9 12.6 - - + -
173B VAL* 3.8 37.7 - - + -
180B VAL* 4.3 2.0 - - + -
181B SER 3.0 12.0 + - - +
184B TRP* 1.3 85.9 - + + +
186B LEU* 1.3 64.7 + - - +
188B TYR* 3.1 5.1 + + + +
189B VAL* 3.0 36.0 + - + +
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Residues in contact with LEU 186 (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 MET* 3.6 53.9 - - + +
125B MET* 3.5 39.0 - - + -
126B GLY* 4.5 3.5 - - - +
129B ILE* 3.5 17.3 - - + +
143B TRP* 4.2 13.9 - - + -
148B MET* 4.7 1.6 - - - -
151B LEU* 4.0 12.3 - - + -
182B ALA* 2.9 26.0 + - + +
183B LEU 3.8 0.4 - - - +
185B PHE* 1.3 73.5 - - + +
187B TRP* 1.3 67.7 + - - +
189B VAL* 3.5 4.3 + - + +
190B LYS* 3.0 24.9 + - - +
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Residues in contact with TRP 187 (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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129B ILE* 3.8 15.8 - - + +
130B PRO 3.9 7.2 - - - -
131B SER* 2.8 33.4 + - - +
134B PRO* 3.5 35.0 - - + +
183B LEU 2.9 14.0 + - - +
184B TRP* 3.4 40.2 - + - +
186B LEU* 1.3 76.2 - - - +
188B TYR* 1.3 91.2 + + - +
190B LYS* 3.2 10.1 + - + +
191B GLN* 2.9 43.0 + - + +
402B PHE* 6.1 0.9 - + - -
407B LEU* 5.3 0.9 - - + -
415B ARG* 6.1 0.9 - - - -
427B GLU 4.9 5.6 - - - -
429B ALA 3.9 17.3 - - - -
430B THR* 5.0 0.2 - - - -
433B SER* 3.6 25.6 - - - -
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Residues in contact with TYR 188 (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 CYS* 3.9 12.3 + - + -
173B VAL* 3.7 25.8 - - + -
184B TRP* 2.8 33.0 + + + +
185B PHE* 3.4 13.2 - - + +
187B TRP* 1.3 92.8 - + + +
189B VAL* 1.3 65.8 + - + +
191B GLN* 3.2 27.4 + - - +
192B CYS* 3.5 8.7 + - - -
198B ILE* 4.1 21.1 - - + -
398B TYR* 5.1 3.6 - - - -
399B THR* 3.7 25.2 - - + +
433B SER* 3.2 25.4 + - - -
434B GLY* 3.5 10.6 + - - -
435B TYR* 3.4 22.6 - + - -
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Residues in contact with VAL 189 (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 MET* 4.9 7.2 - - + +
123B ASP* 4.4 2.2 - - - +
168B PHE* 4.0 10.5 - - + -
185B PHE* 3.0 47.7 + - + +
186B LEU* 4.0 5.2 - - + +
188B TYR* 1.3 77.0 - - + +
190B LYS* 1.3 64.5 + - - +
192B CYS* 3.1 11.8 + - - +
193B GLY 3.5 0.2 + - - -
194B GLY* 3.0 43.2 + - - +
195B THR* 3.7 19.7 - - + +
198B ILE* 4.3 18.2 - - + -
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Residues in contact with LYS 190 (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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123B ASP* 5.9 0.2 - - - -
126B GLY* 3.0 39.2 + - - +
127B ARG* 4.4 8.3 + - - +
129B ILE* 2.8 29.2 + - + +
130B PRO* 4.9 0.6 - - - +
131B SER* 3.2 33.2 + - - +
186B LEU 3.0 17.5 + - - +
187B TRP* 3.2 20.4 + - + +
189B VAL* 1.3 77.9 - - - +
191B GLN* 1.3 58.7 + - + +
192B CYS 3.1 0.2 - - - -
193B GLY* 3.0 19.6 + - - -
194B GLY* 4.1 7.9 - - - +
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Residues in contact with GLN 191 (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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131B SER* 4.1 9.0 - - - +
187B TRP* 2.9 50.3 + - + +
188B TYR* 3.2 25.5 + - - +
190B LYS* 1.3 80.0 - - + +
192B CYS* 1.3 65.1 + - - +
193B GLY 3.4 1.6 - - - -
430B THR 3.6 16.1 - - - +
431B HIS* 3.0 21.7 + - - -
432B TRP 2.9 27.0 + - - -
433B SER* 2.8 57.9 + - - +
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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