Contacts of the strand formed by residues 181 - 190 (chain B) in PDB entry 1XU2
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 ARG 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B VAL* 4.3 14.3 + - - +
174B SER* 3.6 28.3 + - - -
175B ARG 3.5 4.5 - - - +
176B GLU* 3.8 31.8 + - + +
180B ARG* 1.3 76.3 - - - +
182B GLU* 1.3 63.2 + - - +
183B THR* 5.2 3.2 + - - +
217B THR* 4.4 1.8 + - - -
219B LYS* 3.5 44.3 - - - +
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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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174B SER* 3.3 3.9 - - - -
175B ARG* 2.9 72.7 + - + +
180B ARG* 3.8 2.0 + - - +
181B ARG* 1.3 73.9 - - - +
183B THR* 1.3 74.2 + - - +
184B LEU* 3.5 10.7 + - + +
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Residues in contact with THR 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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172B VAL* 3.6 30.2 - - + +
173B VAL 4.0 2.7 - - - +
174B SER* 3.8 9.8 + - - -
181B ARG* 4.3 4.4 + - - +
182B GLU* 1.3 80.8 - - - +
184B LEU* 1.3 64.3 + - - +
185B PHE 4.2 5.4 - - - +
186B ARG* 4.9 2.0 - - - -
232D HIS* 3.3 50.2 - - + +
19S HIS* 5.0 6.2 + - - +
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Residues in contact with LEU 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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156B LEU* 3.9 26.9 - - + -
173B VAL* 2.8 16.6 + - + +
174B SER* 4.3 13.5 - - - +
175B ARG* 4.0 26.0 - - + +
182B GLU* 4.1 17.7 - - - +
183B THR* 1.3 77.7 - - - +
185B PHE* 1.3 68.0 + - + +
208B PHE* 3.5 53.0 - - + -
210B LEU* 4.2 14.6 - - + -
216B ILE* 4.7 0.9 - - + -
110D HIS* 5.3 0.3 + - - -
231D PRO 4.6 3.1 - - - +
232D HIS* 3.6 12.6 - - - +
235D PHE* 4.9 1.2 - - - -
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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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156B LEU* 3.8 28.9 - - + -
157B TYR 4.5 0.2 - - - -
158B SER* 4.1 11.9 - - - -
171B GLN* 5.3 1.8 - - - -
172B VAL* 3.8 0.9 - - - -
173B VAL* 3.0 61.7 + - + +
183B THR* 3.8 2.9 - - - +
184B LEU* 1.3 79.5 - - + +
186B ARG* 1.3 65.6 + - - +
187B CYS 5.1 0.4 - - - -
204B SER* 3.3 47.3 - - - +
205B ALA* 4.1 0.2 - - - -
206B GLY 4.0 4.5 - - - -
208B PHE* 3.5 27.4 - + + -
236B LEU* 6.2 0.2 - - + -
232D HIS* 3.4 11.7 - - - -
235D PHE* 3.7 25.4 - + + -
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Residues in contact with ARG 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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171B GLN 3.2 15.3 - - - +
172B VAL* 4.1 13.5 - - + -
183B THR* 4.9 0.9 - - - -
185B PHE* 1.3 77.6 - - - +
187B CYS* 1.3 59.7 + - - +
188B ILE* 3.6 22.0 - - + +
204B SER* 4.0 5.5 + - - -
159D GLN* 2.7 33.6 + - - +
161D LEU* 3.7 17.5 - - - +
201D SER* 4.4 1.0 + - - -
228D SER* 4.4 0.6 + - - -
230D SER* 3.0 34.6 + - - -
232D HIS* 2.9 37.0 + - - +
233D GLY* 4.2 4.1 - - - +
17S LEU* 3.0 30.6 + - + +
18S LEU 3.7 11.1 + - - -
19S HIS* 3.6 25.8 - - - +
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Residues in contact with CYS 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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170B GLY* 3.1 21.5 - - - -
171B GLN* 3.1 30.5 + - - +
186B ARG* 1.3 74.4 - - - +
188B ILE* 1.3 67.4 + - - +
189B ARG* 3.9 4.5 - - - -
202B CYS* 2.0 57.4 - - - -
203B TYR 3.4 13.5 - - - -
204B SER* 4.1 9.9 - - - -
201D SER* 3.7 11.4 - - - -
17S LEU* 3.6 2.1 - - - +
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Residues in contact with ILE 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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168B THR* 4.4 5.8 - - + -
169B MET 3.6 6.5 - - - +
186B ARG* 3.6 32.5 - - + +
187B CYS* 1.3 81.0 - - - +
189B ARG* 1.3 70.6 + - - +
202B CYS* 3.5 2.4 - - - -
161D LEU* 3.5 25.6 - - + -
199D TYR* 3.9 23.6 - - + +
200D ASN* 3.4 3.6 - - - +
201D SER* 2.9 39.3 + - - +
17S LEU* 3.8 21.1 - - + +
18S LEU* 3.6 26.9 - - + -
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Residues in contact with ARG 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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189A ARG* 3.7 23.7 - - - +
203A TYR 6.0 0.2 + - - -
162B PHE* 5.6 1.8 - - + -
168B THR* 3.3 3.8 - - - -
169B MET* 2.8 39.4 + - + +
187B CYS* 3.9 3.2 - - - -
188B ILE* 1.3 85.7 + - - +
190B SER* 1.3 66.3 + - - +
191B MET* 3.6 5.4 + - - +
200B ASN* 3.6 33.7 - - + -
201B SER 3.3 22.7 + - - +
202B CYS* 3.6 25.2 - - + +
203B TYR* 3.8 10.7 + - - +
189D ARG* 3.4 21.0 - - - +
199D TYR 4.2 1.8 - - - -
200D ASN* 3.5 10.8 - - - -
201D SER* 2.8 36.4 + - - -
202D CYS* 5.1 0.2 - - - +
203D TYR* 5.9 1.8 - - - +
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Residues in contact with SER 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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167B PHE 3.4 8.5 - - - -
168B THR* 4.0 2.6 - - - +
189B ARG* 1.3 74.3 - - - +
191B MET* 1.3 60.3 + - - +
192B PRO* 4.2 1.4 - - - +
200B ASN* 3.3 18.4 + - - -
192D PRO* 3.3 28.0 - - - +
197D ARG 3.0 22.4 + - - -
199D TYR 2.8 21.8 + - - -
200D ASN* 3.0 14.5 + - - +
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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