Contacts of the helix formed by residues 172 - 194 (chain B) in PDB entry 1XJP
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 VAL 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.5 22.5 - - + +
130B GLY* 3.9 24.0 - - - -
131B LYS 4.2 4.3 - - - +
168B TRP* 3.0 68.6 + - + +
171B GLU* 1.3 82.8 - - + +
173B GLY* 1.3 77.0 + - - +
174B LYS 3.1 2.0 - - - -
175B GLN* 2.8 24.4 + - - +
176B LEU* 3.2 10.5 + - + +
502B SER* 5.1 1.8 - - - -
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TRP 3.3 5.2 + - - -
169B ARG* 3.4 14.5 + - - -
172B VAL* 1.3 85.0 - - - +
174B LYS* 1.3 57.4 + - - +
176B LEU* 2.9 32.8 + - - +
177B ARG 3.1 5.2 + - - -
498B CYS* 3.6 24.7 - - - +
502B SER* 4.7 6.3 - - - -
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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
----------------------------------------------------------
169B ARG 3.3 7.6 + - - +
170B SER* 3.3 33.0 + - - +
171B GLU 4.9 0.9 - - - +
172B VAL 3.1 0.6 - - - -
173B GLY* 1.3 75.2 - - - +
175B GLN* 1.3 61.5 + - + +
177B ARG* 3.4 4.6 + - - +
178B PRO* 3.2 18.9 - - - +
496B THR* 3.1 49.9 - - + +
497B TYR* 3.6 35.4 + - - +
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 4.3 27.8 - - + +
130B GLY* 5.6 3.8 - - - -
171B GLU* 3.1 25.5 + - - +
172B VAL* 2.8 21.6 + - - +
174B LYS* 1.3 77.2 - - + +
176B LEU* 1.3 62.2 + - - +
178B PRO* 3.3 12.4 - - - +
179B LEU* 3.7 16.3 - - + +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 3.9 28.0 - - + +
126B ILE* 3.1 44.4 - - + -
127B TYR* 5.2 4.5 - - + -
172B VAL* 3.2 8.7 + - + +
173B GLY* 2.9 14.5 + - - +
175B GLN* 1.3 82.5 - - - +
177B ARG* 1.3 57.1 + - - +
178B PRO 3.4 0.2 - - - -
179B LEU* 3.2 7.5 + - + +
180B TYR* 2.8 32.6 + - - +
498B CYS* 4.4 0.4 - - - -
501B ALA* 3.5 42.6 - - + +
502B SER* 4.7 2.5 - - - +
507B SER* 4.3 10.8 - - - +
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY 3.1 6.0 + - - +
174B LYS 3.6 7.9 - - - +
176B LEU* 1.3 77.6 - - - +
178B PRO* 1.3 71.3 - - + +
180B TYR* 3.3 1.4 + - - +
181B GLU* 2.6 55.4 + - - +
470B LYS* 2.6 33.7 + - - +
473B TRP* 3.5 25.2 - - - +
474B MET* 4.0 3.0 - - - +
495B GLU* 2.8 50.2 + - - +
496B THR* 3.7 14.1 - - - +
497B TYR 3.1 19.1 + - - +
498B CYS* 3.7 21.9 - - + +
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Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS 3.2 13.7 - - - +
175B GLN* 3.3 13.0 - - - +
177B ARG* 1.3 98.9 - - + +
179B LEU* 1.3 65.6 + - + +
181B GLU* 3.5 11.4 + - - +
182B GLU* 3.4 20.8 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 4.7 12.1 - - - +
119B ILE* 3.6 27.2 - - + +
122B THR* 3.8 33.2 - - + -
123B MET* 3.7 26.0 - - + +
126B ILE* 4.9 3.6 - - + -
175B GLN* 3.7 19.1 - - + +
176B LEU* 3.2 14.3 + - + +
178B PRO* 1.3 79.8 - - + +
180B TYR* 1.3 58.9 + - - +
182B GLU* 3.3 5.6 + - - +
183B TYR* 2.9 28.8 + - - +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 3.8 16.5 - - - -
176B LEU 2.8 21.2 + - - +
177B ARG 3.7 4.3 - - - +
179B LEU* 1.3 74.1 - - - +
181B GLU* 1.3 62.1 + - - +
183B TYR* 3.2 38.8 + + - +
184B VAL* 3.0 34.7 + - + +
459B TRP* 4.2 19.9 - + - -
460B ARG* 4.1 18.9 + - - +
463B VAL* 5.2 1.8 - - + -
464B PHE* 4.2 7.6 - - - -
473B TRP* 3.8 19.1 - + + -
498B CYS* 4.1 19.1 - - - -
500B PRO* 5.7 0.2 - - + -
501B ALA* 4.4 5.2 - - + -
506B VAL* 3.6 41.8 + - + +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 2.6 49.6 + - - +
178B PRO* 3.8 10.4 - - - +
179B LEU 3.3 0.2 - - - -
180B TYR* 1.3 72.6 - - - +
182B GLU* 1.3 68.5 + - - +
184B VAL* 3.1 19.6 - - - +
185B VAL* 3.4 9.9 + - - +
470B LYS* 3.2 34.0 + - + +
473B TRP* 3.4 29.2 - - + -
495B GLU 5.0 0.2 - - - +
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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
----------------------------------------------------------
115B ARG* 2.7 50.2 + - - +
119B ILE* 3.3 22.1 - - + +
178B PRO 3.4 10.1 + - - +
179B LEU* 3.3 7.1 + - - +
181B GLU* 1.3 78.8 - - - +
183B TYR* 1.3 63.0 + - - +
185B VAL* 3.2 11.7 + - + +
186B LEU* 3.1 30.5 + - + +
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.4 6.3 - - + -
119B ILE* 4.0 15.6 - - + +
120B LEU* 3.8 17.5 - - + -
123B MET* 3.6 18.2 - - + -
179B LEU 2.9 14.2 + - - +
180B TYR* 3.3 49.5 + + - +
181B GLU 3.1 0.2 - - - -
182B GLU* 1.3 73.8 - - - +
184B VAL* 1.3 76.4 + - + +
186B LEU* 3.5 5.0 + - - +
187B LYS* 2.9 43.2 + - + +
199B TYR* 3.4 14.9 - + - -
203B TRP* 4.3 6.2 - - - -
460B ARG* 4.9 0.7 + - - -
464B PHE* 4.3 8.3 - + - -
506B VAL 4.6 2.1 + - - -
509B ASP* 2.6 37.8 + - + +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 3.0 32.5 + - + +
181B GLU* 3.1 17.5 - - - +
183B TYR* 1.3 84.1 - - + +
185B VAL* 1.3 61.1 + - + +
187B LYS* 3.7 3.9 - - - +
188B ASN* 2.7 45.7 + - - +
463B VAL* 4.0 14.8 - - + +
464B PHE* 3.6 30.1 - - + -
470B LYS* 4.8 3.1 - - - +
473B TRP* 4.3 12.6 - - + -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU 3.5 14.4 - - - +
182B GLU* 3.2 12.3 + - + +
184B VAL* 1.3 84.8 - - + +
186B LEU* 1.3 71.0 + - + +
188B ASN* 3.3 5.6 + - - +
189B GLU* 3.0 34.0 + - - +
192B ARG* 5.1 1.8 + - - +
470B LYS* 4.3 14.6 - - - +
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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
----------------------------------------------------------
108B LEU* 4.3 9.2 - - + +
112B LYS* 4.0 32.5 - - + +
115B ARG* 4.1 11.9 - - + -
116B LEU* 4.1 37.2 - - + +
119B ILE* 4.1 22.0 - - + -
182B GLU* 3.1 22.2 + - + +
183B TYR 3.9 3.8 - - - +
185B VAL* 1.3 89.8 - - + +
187B LYS* 1.3 58.2 + - - +
189B GLU* 3.4 12.6 - - - +
190B MET* 3.0 25.3 + - - +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 5.2 5.1 + - - -
116B LEU* 3.9 33.3 - - + +
120B LEU* 4.5 5.3 - - - +
183B TYR* 2.9 36.6 + - + +
184B VAL* 3.7 6.1 - - - +
186B LEU* 1.3 74.9 - - - +
188B ASN* 1.3 60.9 + - - +
189B GLU 3.1 1.6 - - - -
190B MET* 3.2 12.5 + - + +
191B ALA* 2.9 28.6 + - - +
199B TYR* 2.8 68.9 + - + +
509B ASP* 3.0 18.5 + - - -
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 2.7 27.6 + - - +
185B VAL* 3.8 4.6 - - - +
187B LYS* 1.3 74.4 - - - +
189B GLU* 1.3 57.7 + - - +
191B ALA* 3.4 1.4 + - - +
192B ARG* 2.9 52.4 + - - +
198B ASP* 3.0 12.3 - - - +
199B TYR* 2.7 37.0 + - - +
463B VAL 4.7 2.2 + - - -
464B PHE* 2.9 32.8 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.1 16.1 - - + +
112B LYS* 2.6 32.2 + - - -
185B VAL* 3.0 24.6 + - - +
186B LEU* 3.4 16.1 - - - +
188B ASN* 1.3 76.1 - - - +
190B MET* 1.3 69.0 + - - +
192B ARG* 3.4 24.0 + - - +
193B ALA* 3.1 24.3 + - + +
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY* 3.1 30.1 - - - +
105B SER* 3.8 10.3 - - - +
107B VAL* 4.0 9.0 - - - -
108B LEU* 4.2 14.7 - - + +
116B LEU* 5.5 0.9 - - + -
186B LEU 3.0 13.5 + - - +
187B LYS* 3.5 17.7 - - + +
189B GLU* 1.3 76.6 - - - +
191B ALA* 1.3 82.5 + - - +
193B ALA* 3.3 2.3 + - - +
194B ASN* 2.7 51.6 + - - +
199B TYR* 4.7 8.7 - - - -
202B TYR* 3.2 47.6 - - + +
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Residues in contact with ALA 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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187B LYS 2.9 16.2 + - - +
188B ASN 3.6 2.9 - - - +
190B MET* 1.3 93.4 - - + +
192B ARG* 1.3 62.8 + - - +
194B ASN* 3.0 9.6 + - - +
195B HIS 3.3 0.5 + - - -
196B TYR* 3.0 25.0 + - + +
198B ASP* 3.5 10.5 - - - +
199B TYR* 3.5 30.1 - - - +
202B TYR* 4.2 6.1 - - + -
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Residues in contact with ARG 192 (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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185B VAL* 5.1 2.0 + - - +
188B ASN* 2.9 50.5 + - - +
189B GLU* 3.4 28.8 + - - +
191B ALA* 1.3 72.4 - - - +
193B ALA* 1.3 56.3 + - - +
195B HIS* 2.7 28.2 + - - -
196B TYR 3.1 9.9 + - - +
197B GLU 3.5 22.7 + - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 3.8 33.6 - - + +
108B LEU* 6.2 0.9 - - + -
189B GLU* 3.1 17.1 + - + +
190B MET 3.7 3.4 - - - +
192B ARG* 1.3 77.8 - - - +
194B ASN* 1.3 57.6 + - - +
195B HIS* 3.2 18.2 + - - -
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Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 5.4 2.6 - - - +
103B ASN* 3.8 14.7 + - - +
104B GLY* 2.9 37.6 + - - -
107B VAL* 3.4 8.3 - - - +
190B MET* 2.7 46.9 + - + +
191B ALA 3.0 8.9 + - - +
192B ARG 3.0 1.0 - - - -
193B ALA* 1.3 77.4 - - - +
195B HIS* 1.3 78.0 + - - +
196B TYR* 3.4 20.8 - - + -
202B TYR* 4.9 1.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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