Contacts of the strand formed by residues 182 - 197 (chain A) in PDB entry 1S8B
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 TYR 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LYS* 2.6 32.6 + - - -
156A ARG* 3.1 8.3 - - + -
166A ASN* 2.9 26.2 - - - -
169A PRO* 3.3 19.3 - - + +
170A ALA 4.8 0.2 + - - -
171A ASN* 3.2 33.3 - - + +
180A THR* 4.4 0.2 + - - -
181A GLN* 1.3 90.9 - - + +
183A CYS* 1.3 60.0 + - - +
184A TYR* 2.8 31.0 - + + -
191A LEU* 3.7 0.4 - - + -
194A LEU* 3.0 15.0 - - + -
195A SER 6.0 0.2 - - - -
196A VAL* 4.6 0.7 - - + -
202A PHE 3.0 1.3 + - - +
203A PHE* 3.3 34.9 - + + -
204A GLN* 2.9 29.8 + - - +
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Residues in contact with CYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 5.4 5.2 - - + -
156A ARG 3.0 8.3 + - - +
157A ALA* 3.2 10.5 - - + +
158A HIS 2.8 24.7 + - - -
180A THR* 2.6 31.9 - - - -
182A TYR* 1.3 70.1 - - - +
184A TYR* 1.3 68.3 + - - +
200A PHE* 4.8 0.4 - - - -
204A GLN* 2.6 43.7 - - + -
206A LEU* 4.5 12.8 - - + -
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.8 18.7 - - - -
158A HIS* 2.6 32.7 - + - -
161A TYR* 2.5 31.2 - + - +
166A ASN* 2.6 28.6 + - + -
182A TYR* 2.8 35.9 - + + -
183A CYS* 1.3 103.9 - - - +
185A SER* 1.3 60.5 + - - +
189A LEU* 5.0 3.6 - - + -
191A LEU* 3.6 24.5 - - + -
204A GLN 3.0 10.6 + - - +
205A GLU* 3.3 10.8 - - + +
206A LEU* 3.0 24.1 + - - +
212A VAL* 6.4 1.3 - - + -
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Residues in contact with SER 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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158A HIS 3.1 11.4 + - - +
159A THR* 4.4 0.7 - - - -
160A PRO* 3.1 28.0 - - - +
161A TYR* 3.3 1.0 - - - -
184A TYR* 1.3 77.3 - - - +
186A ILE* 1.3 75.7 - - - +
189A LEU* 5.5 0.7 - - - -
206A LEU* 3.5 25.3 - - - +
207A VAL 4.4 6.2 + - - -
208A ILE 3.5 13.9 - - - -
209A ALA* 4.2 3.1 - - - -
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO* 2.9 36.1 - - + +
161A TYR* 2.4 38.8 - - + +
162A ILE* 2.9 20.0 - - + -
185A SER* 1.3 84.4 - - - +
187A GLN* 1.3 68.3 + - + +
189A LEU* 2.9 26.7 - - + +
208A ILE* 3.1 17.5 + - - -
209A ALA* 3.0 6.1 - - - +
210A GLY 2.9 24.1 + - - +
212A VAL* 4.3 1.7 - - - +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 4.6 14.4 - - - +
162A ILE* 2.9 68.0 - - + +
163A ASN* 3.1 4.9 + - - +
186A ILE* 1.3 87.1 - - + +
188A SER* 1.3 65.4 + - - +
189A LEU* 3.5 4.3 - - - +
210A GLY* 3.0 16.6 - - - +
211A ILE* 5.8 0.2 - - + -
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.7 21.5 + - - +
6A ASN* 3.1 33.2 + - - -
7A SER 4.2 4.2 + - - -
163A ASN* 2.8 42.9 + - - -
164A ILE 3.1 2.1 + - - +
187A GLN* 1.3 77.0 - - - +
189A LEU* 1.3 60.1 + - - +
210A GLY 3.1 2.8 + - - -
211A ILE* 3.0 23.6 + - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.7 2.6 - - - +
161A TYR* 2.8 44.2 - - + +
162A ILE 3.7 0.7 - - - -
163A ASN 3.6 4.9 - - - +
164A ILE* 2.9 47.8 - - + +
184A TYR* 5.0 2.9 - - + -
185A SER 4.9 0.7 - - - -
186A ILE* 2.9 24.2 - - + -
187A GLN 3.6 6.3 - - - +
188A SER* 1.3 77.4 - - - +
190A PHE* 1.3 61.5 + - - +
191A LEU* 4.1 1.8 - - + -
211A ILE 3.3 4.3 + - - +
212A VAL* 3.4 17.8 - - + +
213A GLU* 3.0 25.5 + - - +
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.0 28.9 - - - +
9A ASN* 3.5 6.5 - - - +
164A ILE 2.8 8.7 + - - -
165A TYR* 2.7 49.5 - + - -
166A ASN 2.8 25.2 + - - -
167A CYS* 4.3 4.5 - - - -
189A LEU* 1.3 73.2 - - - +
191A LEU* 1.3 59.9 + - - +
192A GLY* 4.4 6.7 - - - -
213A GLU* 3.2 41.3 - - + -
215A GLU* 2.6 39.0 - - + -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 3.2 8.1 - - + +
182A TYR* 3.7 6.7 - - + -
184A TYR* 3.6 34.5 - - + -
189A LEU* 4.1 2.2 - - + +
190A PHE* 1.3 75.0 - - - +
192A GLY* 1.3 62.3 + - - +
194A LEU* 3.5 17.0 - - + -
203A PHE* 3.1 48.0 - - + -
213A GLU 2.9 11.0 + - - +
214A ASN* 3.0 35.5 - - + +
215A GLU* 3.0 25.2 + - - +
217A LYS* 5.2 1.3 - - + -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 5.1 0.2 - - - -
166A ASN 3.0 5.3 + - - -
167A CYS* 2.7 14.6 - - - -
190A PHE* 4.4 8.3 - - - -
191A LEU* 1.3 78.2 - - - +
193A ILE* 1.3 74.8 + - - +
194A LEU* 2.6 23.1 - - - +
215A GLU* 2.9 15.3 - - - -
216A TRP* 4.9 0.7 - - - -
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.5 4.9 - - - +
167A CYS* 3.3 11.9 - - + -
168A GLU* 2.9 58.5 + - + +
169A PRO* 3.0 4.3 - - - +
192A GLY* 1.3 79.8 - - - +
194A LEU* 1.3 61.1 + - - +
215A GLU 3.4 1.2 + - - -
216A TRP* 2.9 49.4 + - + -
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Residues in contact with LEU 194 (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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166A ASN* 3.5 12.8 - - - +
167A CYS* 3.2 7.4 - - - -
169A PRO* 2.9 28.7 - - + +
182A TYR* 3.0 37.2 - - + -
191A LEU* 3.5 9.4 - - + -
192A GLY 2.6 37.0 - - - +
193A ILE* 1.3 80.9 - - - +
195A SER* 1.3 60.9 + - - +
203A PHE* 2.9 30.7 - - + -
216A TRP 3.4 3.5 + - - +
217A LYS* 3.5 4.2 - - - +
218A ARG* 3.0 24.7 + - - +
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Residues in contact with SER 195 (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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169A PRO 3.2 9.5 + - - +
170A ALA* 3.6 8.0 - - - -
171A ASN* 2.9 27.1 + - - +
182A TYR* 6.0 0.2 - - - -
194A LEU* 1.3 75.5 - - - +
196A VAL* 1.3 66.3 + - - +
197A MET* 5.4 5.3 - - - +
218A ARG* 2.9 54.3 + - - +
220A CYS* 4.4 7.8 - - - +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.3 7.6 - - + -
181A GLN* 2.8 53.2 - - + +
182A TYR* 4.5 0.7 - - + -
195A SER* 1.3 79.6 + - - +
197A MET* 1.3 60.4 + - - +
202A PHE* 2.8 23.7 - - + +
203A PHE* 3.2 36.8 - - + -
218A ARG 3.0 1.6 + - - -
219A THR 3.7 0.5 - - - -
220A CYS* 3.0 26.7 + - - +
222A ARG* 3.1 18.4 - - - +
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Residues in contact with MET 197 (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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149A MET* 5.4 0.2 - - - -
170A ALA* 6.3 0.2 - - + -
171A ASN 2.8 6.0 + - - +
172A PRO* 3.0 45.3 - - + -
173A SER 2.7 29.1 + - - +
181A GLN* 2.7 20.9 + - - -
195A SER* 5.4 6.5 - - - +
196A VAL* 1.3 77.4 - - - +
198A LEU* 1.3 56.1 + - - +
220A CYS* 3.4 23.1 - - + +
221A SER* 3.3 7.2 - - - +
222A ARG* 3.8 0.4 - - - +
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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