Contacts of the strand formed by residues 181 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A SER* 4.5 13.6 + - - -
175A ARG 3.7 3.6 - - - +
176A GLU* 4.0 31.2 - - + +
180A ARG* 1.3 75.5 - - - +
182A GLU* 1.3 64.9 + - - +
183A THR* 4.0 25.3 + - - +
219A LYS* 6.3 0.9 - - - +
19R HIS* 5.6 5.1 + - - -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.3 4.9 - - - -
175A ARG* 3.0 73.1 + - + +
180A ARG* 5.4 0.9 - - + +
181A ARG* 1.3 77.6 - - - +
183A THR* 1.3 74.2 + - - +
184A LEU* 3.5 17.1 + - + +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.7 28.1 - - + +
173A VAL 3.9 6.5 - - - +
174A SER* 4.0 8.5 + - - -
181A ARG* 4.0 19.6 + - - +
182A GLU* 1.3 79.4 - - - +
184A LEU* 1.3 63.6 + - - +
185A PHE 4.1 6.3 - - - +
186A ARG* 4.2 1.6 - - + -
232B HIS* 3.3 54.5 + - + +
19R HIS* 4.9 5.9 + - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.1 25.6 - - + -
173A VAL* 2.8 16.8 + - + +
174A SER 4.3 6.1 - - - +
175A ARG* 3.9 21.1 - - + +
182A GLU* 3.6 34.8 - - + +
183A THR* 1.3 73.4 - - - +
185A PHE* 1.3 67.5 + - + +
208A PHE* 3.6 53.1 - - + -
209A HIS 6.0 0.7 - - - +
210A LEU* 4.2 15.0 - - + -
216A ILE* 4.6 1.3 - - + -
110B HIS* 5.2 0.2 + - - -
231B PRO 4.4 3.5 - - - +
232B HIS* 3.4 13.2 - - - +
235B PHE* 4.8 1.6 - - - -
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Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.7 31.2 - - + -
157A TYR 4.6 0.2 - - - -
158A SER* 4.0 11.7 - - - -
171A GLN* 4.1 2.4 - - + +
172A VAL* 3.7 1.2 - - - -
173A VAL* 2.9 62.3 + - + +
183A THR* 3.8 1.2 - - - +
184A LEU* 1.3 80.4 - - + +
186A ARG* 1.3 64.7 + - - +
187A CYS 5.0 0.4 - - - -
204A SER* 3.5 46.9 - - - +
205A ALA 4.3 4.5 - - - -
206A GLY 4.1 1.6 - - - -
208A PHE* 3.6 27.4 - + + -
236A LEU* 6.2 0.4 - - + -
232B HIS* 3.4 9.6 - - - -
235B PHE* 3.7 24.0 - + + -
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLN 3.2 6.7 - - - +
172A VAL* 4.0 21.1 - - + -
183A THR* 4.2 3.1 - - + -
185A PHE* 1.3 81.5 - - - +
187A CYS* 1.3 59.8 + - - +
188A ILE* 3.7 20.6 + - + +
204A SER* 4.0 1.0 + - - -
159B GLN* 2.8 28.6 + - - +
161B LEU* 3.6 21.1 - - - +
201B SER* 4.3 1.7 + - - -
228B SER* 4.4 0.8 + - - -
230B SER* 3.0 34.6 + - - -
232B HIS* 3.0 32.3 + - + +
233B GLY* 3.9 4.7 - - - -
17R LEU* 2.8 38.2 + - + -
18R LEU 3.7 18.4 + - - -
19R HIS* 3.8 19.7 + - - +
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Residues in contact with CYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY* 3.1 5.2 - - - -
171A GLN* 3.0 49.6 + - + +
185A PHE* 5.0 0.6 - - - -
186A ARG* 1.3 74.1 - - - +
188A ILE* 1.3 66.2 + - - +
189A ARG* 3.9 4.0 - - - -
202A CYS* 2.0 58.1 - - - -
203A TYR 3.4 14.4 - - - -
204A SER* 4.0 10.3 - - - -
159B GLN* 5.4 0.2 - - - -
201B SER* 3.7 9.9 - - - -
17R LEU* 3.7 0.9 - - - +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 4.5 4.9 - - + -
169A MET 3.6 6.1 - - - +
186A ARG* 3.7 33.2 - - + +
187A CYS* 1.3 79.7 - - - +
189A ARG* 1.3 74.3 + - - +
202A CYS* 3.9 0.7 - - - -
161B LEU* 3.6 25.4 - - + -
199B TYR* 3.9 24.7 - - + +
200B ASN* 3.5 1.5 - - - +
201B SER* 2.9 37.1 + - - +
17R LEU* 3.7 23.3 - - + +
18R LEU* 3.8 25.4 - - + -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 5.5 1.6 - - + -
168A THR* 3.4 3.9 - - - -
169A MET* 2.8 38.4 + - + +
187A CYS* 3.9 2.4 - - - -
188A ILE* 1.3 88.4 + - - +
190A SER* 1.3 67.1 + - - +
191A MET* 3.7 7.9 + - - +
200A ASN* 3.6 30.5 - - + +
201A SER 3.1 23.3 + - - +
202A CYS* 3.8 24.7 - - + +
203A TYR 4.6 3.4 + - - +
189B ARG* 3.7 17.8 - - - +
199B TYR 4.2 1.8 - - - -
200B ASN* 3.4 14.0 + - - -
201B SER* 2.6 36.3 + - - -
203B TYR 5.5 0.4 - - - +
189D ARG* 3.5 34.5 - - - +
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE 3.4 7.6 - - - -
168A THR* 4.0 2.6 - - - +
189A ARG* 1.3 75.9 - - - +
191A MET* 1.3 61.2 + - - +
192A PRO* 4.3 0.5 - - - +
200A ASN* 3.2 19.1 + - - -
192B PRO* 3.3 25.5 - - - +
197B ARG 3.1 22.1 + - - -
199B TYR 2.8 20.7 + - - -
200B ASN* 2.9 17.5 + - - +
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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