Contacts of the strand formed by residues 180 - 192 (chain A) in PDB entry 1D0G
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 GLY 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLU 3.8 1.8 + - - -
179A LYS* 1.3 79.0 - - - +
181A PHE* 1.3 65.0 + - - -
182A TYR* 3.3 10.8 - - - -
249A GLU* 3.4 4.1 - - - -
250A LEU 2.9 31.8 + - - -
279A LEU* 4.0 7.6 - - - -
121B ARG* 4.0 15.0 - - - -
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Residues in contact with PHE 181 (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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180A GLY* 1.3 69.6 - - - -
182A TYR* 1.3 60.6 + - - +
247A ILE* 3.8 4.3 - - + -
248A PHE 3.7 1.3 - - - -
249A GLU* 3.9 36.3 - - + -
279A LEU* 3.4 8.3 - - - +
280A VAL* 2.8 51.4 + - + +
121B ARG* 3.4 52.0 - - + +
123B ALA* 4.4 7.0 - - + -
163B PHE* 3.5 48.7 - + + -
165B SER* 4.0 18.6 - - - -
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Residues in contact with TYR 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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122A VAL* 3.6 26.6 - - + +
167A LEU* 4.6 7.6 - - + +
176A ILE* 3.5 27.8 - - + +
177A HIS 4.8 0.7 + - - -
178A GLU* 2.5 34.0 + - - +
180A GLY 3.3 24.0 - - - -
181A PHE* 1.3 73.8 - - - +
183A TYR* 1.3 62.9 + - - +
184A ILE* 3.3 14.1 + - + +
246A GLY 3.4 0.2 - - - +
247A ILE* 3.3 4.2 - - - +
248A PHE 2.8 36.2 + - - +
250A LEU* 3.8 26.0 - - + -
277A ALA* 4.4 7.0 - - + -
278A PHE* 3.4 21.1 - - - -
279A LEU* 3.6 27.9 - - + +
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Residues in contact with TYR 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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182A TYR* 1.3 69.9 - - - +
184A ILE* 1.3 57.9 + - - +
185A TYR* 3.6 26.6 + + + -
243A TYR* 2.8 19.9 + - - -
245A GLY* 3.6 10.0 - - - -
246A GLY* 3.4 28.3 - - - -
247A ILE* 4.1 5.4 - - + +
277A ALA* 3.2 3.5 - - - -
278A PHE* 2.9 54.6 + + + -
280A VAL* 3.6 25.5 - - + +
183B TYR* 4.0 13.7 - + - -
185B TYR* 4.5 3.8 - + - -
243B TYR* 2.7 30.3 + - - -
278B PHE* 3.8 15.3 - + + -
183D TYR* 3.8 12.0 + + - -
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Residues in contact with ILE 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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182A TYR* 3.6 22.4 - - + +
183A TYR* 1.3 76.2 - - - +
185A TYR* 1.3 65.0 + - - +
210A ILE* 4.0 16.4 - - + -
222A LEU* 3.7 28.3 - - + -
223A MET* 3.5 6.2 - - + +
245A GLY* 3.1 2.8 - - - -
246A GLY 2.9 29.5 + - - +
248A PHE* 4.0 13.5 - - + -
250A LEU* 4.0 20.0 - - + -
256A ILE* 3.9 24.7 - - + -
275A PHE* 4.0 13.7 - - + -
276A GLY 3.5 12.3 - - - +
277A ALA* 4.1 1.8 - - + -
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Residues in contact with TYR 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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125A HIS* 2.6 24.9 + - - -
183A TYR* 3.6 23.3 - + + -
184A ILE* 1.3 75.8 - - - +
186A SER* 1.3 68.8 + - - +
210A ILE* 4.2 5.2 - - - -
243A TYR* 3.3 34.1 - + + +
244A GLN 3.3 10.8 - - - +
245A GLY* 4.0 0.4 - - - -
274A PHE* 3.7 23.6 - + - -
275A PHE* 3.4 3.6 - - - -
276A GLY* 2.9 61.1 + - - +
277A ALA* 3.8 3.6 - - - -
278A PHE* 4.5 1.6 - + - -
183D TYR* 4.4 6.3 - + - -
245D GLY 3.9 0.9 - - - -
246D GLY* 3.8 13.5 - - - -
247D ILE* 3.0 32.2 + - + +
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Residues in contact with SER 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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154A TRP* 4.6 1.2 - - - -
185A TYR* 1.3 81.5 - - - +
187A GLN* 1.3 63.1 + - - +
188A THR* 4.0 1.9 - - - +
208A GLN* 3.2 32.1 + - - +
210A ILE* 3.8 8.2 - - - +
243A TYR* 3.4 5.6 - - - -
244A GLN 3.1 24.9 + - - -
258A VAL* 3.5 28.5 - - - +
274A PHE 2.9 17.7 + - - -
275A PHE* 4.0 1.3 - - - -
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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
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154A TRP* 4.7 0.3 - - - -
186A SER* 1.3 75.0 - - - +
188A THR* 1.3 69.3 + - - +
241A SER* 4.2 6.2 - - - -
242A ILE 3.2 10.8 - - - +
243A TYR* 3.7 16.3 + - + +
272A ALA 3.3 11.5 + - - +
273A SER* 3.2 3.3 - - - -
274A PHE* 2.9 70.2 + - + +
224D LYS 3.1 15.8 + - - -
225D SER* 3.4 18.4 + - - -
243D TYR 4.3 0.3 - - - +
244D GLN* 3.0 36.7 + - - +
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Residues in contact with THR 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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151A ILE* 4.1 17.0 - - + -
154A TRP* 5.2 2.2 - - + -
186A SER* 4.0 8.3 - - - +
187A GLN* 1.3 79.5 - - - +
189A TYR* 1.3 61.3 + - - +
190A PHE* 3.6 14.3 + - - -
208A GLN* 3.2 33.1 + - + +
240A TYR 3.7 1.0 - - - +
242A ILE* 2.9 28.8 + - - +
258A VAL* 4.1 1.3 - - + -
260A VAL* 3.9 24.2 - - + -
266A ILE* 4.2 9.2 - - + -
272A ALA 4.4 0.7 - - - -
273A SER* 3.7 5.8 - - - +
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Residues in contact with TYR 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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188A THR* 1.3 69.0 - - - +
190A PHE* 1.3 76.2 + - - +
191A ARG* 3.3 28.1 - - + -
239A LEU* 3.7 12.6 - - - +
240A TYR 3.9 9.0 - - - -
241A SER* 3.4 26.7 - - - +
266A ILE* 3.4 5.5 - - - +
267A ASP* 2.9 45.8 + - + +
272A ALA* 3.5 31.1 + - + +
273A SER* 3.0 18.8 + - - +
224D LYS* 3.9 10.8 - - + -
226D ALA* 3.8 11.1 - - + +
98R GLU* 2.8 35.4 + - - +
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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
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188A THR* 3.6 25.4 - - - -
189A TYR* 1.3 75.3 - - - +
191A ARG* 1.3 58.4 + - - +
192A PHE* 5.2 1.6 - - + -
206A MET* 3.6 48.2 - - + -
207A VAL 4.0 18.2 - - - -
238A GLY 3.8 0.8 - - - +
239A LEU* 3.7 0.7 - - - -
240A TYR* 2.8 49.4 + - - +
242A ILE* 3.8 18.2 - - + -
260A VAL* 4.0 2.7 - - + -
261A THR 3.3 26.5 - - - -
262A ASN* 3.8 13.0 - - + -
265A LEU* 3.6 13.2 - - + -
266A ILE* 3.5 21.3 - - + -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 4.0 9.1 - - - +
189A TYR* 3.3 35.7 + - + -
190A PHE* 1.3 75.4 - - - +
192A PHE* 1.3 65.5 + - - +
193A GLN* 5.2 1.0 + - - +
238A GLY 3.4 5.4 - - - -
239A LEU* 4.3 1.1 - - - -
265A LEU* 2.9 27.8 + - - +
267A ASP* 3.4 26.8 + - + +
224D LYS* 5.8 0.2 - - - +
67R ASP* 2.6 46.7 + - - +
68R SER* 5.2 4.8 + - - -
98R GLU* 3.3 25.2 + - - -
99R MET* 3.1 30.2 - - + +
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Residues in contact with PHE 192 (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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190A PHE 5.2 0.2 - - - -
191A ARG* 1.3 82.4 - - - +
193A GLN* 1.3 58.4 + - - +
194A GLU* 2.9 46.7 - - + +
204A LYS* 3.6 23.1 - - + -
206A MET* 4.1 9.2 - - - -
229A SER* 4.1 9.4 - - - -
235A ALA* 6.3 2.7 - - + -
237A TYR* 3.2 9.5 - - - +
238A GLY* 2.8 56.3 + - - +
240A TYR* 3.9 25.8 - + - -
265A LEU* 3.6 27.6 - - + -
99R MET* 4.0 5.1 - - - +
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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