Contacts of the strand formed by residues 180 - 192 (chain K) in PDB entry 1DU3
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178K GLU 3.8 2.0 + - - -
179K LYS* 1.3 76.6 - - - +
181K PHE* 1.3 70.2 + - - -
182K TYR* 3.2 7.3 - - - -
249K GLU* 3.5 11.1 - - - +
250K LEU 3.1 29.2 + - - -
279K LEU* 4.2 6.1 - - - -
281K GLY 4.2 11.4 - - - -
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Residues in contact with PHE 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K GLY* 1.3 76.0 - - - -
182K TYR* 1.3 59.0 + - - +
247K ILE* 3.8 9.2 - - + -
248K PHE 3.5 3.1 - - - -
249K GLU* 4.1 32.1 - - + -
279K LEU* 2.9 20.3 - - - +
280K VAL* 3.1 25.4 + - + +
281K GLY* 3.1 35.7 - - - -
121L ARG* 3.7 17.3 - - + -
123L ALA* 4.2 8.5 - - + -
163L PHE* 3.5 46.2 - + + -
165L SER* 3.9 15.7 - - - -
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Residues in contact with TYR 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K VAL* 3.5 31.5 - - + +
167K LEU* 4.4 8.5 - - + +
176K ILE* 3.7 26.6 - - + +
177K HIS 4.8 1.0 + - - -
178K GLU* 2.8 36.2 + - - +
180K GLY 3.2 26.5 - - - -
181K PHE* 1.3 76.4 - - - +
183K TYR* 1.3 62.8 + - - +
184K ILE* 3.5 11.0 + - + +
246K GLY 3.4 1.6 - - - +
247K ILE* 3.1 7.8 - - - +
248K PHE 2.9 28.7 + - - +
250K LEU* 3.8 26.2 - - + -
277K ALA* 4.5 7.9 - - + -
278K PHE* 3.1 21.8 - - - +
279K LEU* 3.3 21.0 - - + +
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Residues in contact with TYR 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J TYR* 4.2 9.2 - + - -
182K TYR* 1.3 72.8 - - - +
184K ILE* 1.3 58.0 + - - +
185K TYR* 3.9 16.8 - + + -
243K TYR* 3.0 25.3 + - - -
245K GLY* 3.2 14.6 - - - -
246K GLY* 3.2 27.4 - - - -
247K ILE* 4.2 6.1 - - + +
277K ALA* 2.9 5.5 - - - +
278K PHE* 2.8 74.9 + + + -
280K VAL* 3.9 5.5 - - + +
183L TYR* 3.7 15.1 + + - -
185L TYR* 4.1 6.3 - + - -
243L TYR* 2.5 28.8 + - - -
278L PHE* 3.9 19.3 - + + -
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Residues in contact with ILE 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K TYR* 3.8 15.0 - - + +
183K TYR* 1.3 79.1 - - - +
185K TYR* 1.3 63.9 + - - +
210K ILE* 4.1 18.2 - - + -
222K LEU* 4.1 24.2 - - + -
223K MET* 3.3 8.2 - - + +
245K GLY* 3.0 20.5 - - - -
246K GLY 2.8 14.4 + - - +
248K PHE* 4.3 11.7 - - + -
250K LEU* 4.1 22.2 - - + -
256K ILE* 4.3 13.7 - - + -
275K PHE* 3.9 20.0 - - + -
276K GLY 3.6 10.1 - - - +
277K ALA* 3.9 9.9 - - + -
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Residues in contact with TYR 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J TYR* 4.3 7.4 - + - -
245J GLY 3.9 0.9 - - - -
246J GLY* 3.7 15.5 - - - -
247J ILE* 3.0 39.8 + - + +
125K HIS* 2.9 24.3 + - - +
183K TYR* 3.9 19.7 - + + -
184K ILE* 1.3 76.2 - - - +
186K SER* 1.3 71.6 + - - +
210K ILE* 4.2 4.5 - - - -
243K TYR* 3.2 36.3 - + + +
244K GLN 3.1 11.7 - - - +
274K PHE* 3.7 22.9 - + - -
275K PHE* 3.3 3.5 - - - -
276K GLY* 3.0 47.8 + - - +
277K ALA* 3.9 2.0 - - - -
278K PHE* 4.7 1.8 - + - -
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Residues in contact with SER 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K TRP* 4.7 0.3 - - - -
185K TYR* 1.3 85.6 - - - +
187K GLN* 1.3 60.1 + - - +
188K THR* 3.7 12.5 - - - +
208K GLN* 3.1 35.4 + - - +
210K ILE* 4.0 3.0 - - - +
242K ILE 3.2 4.2 - - - +
243K TYR* 3.5 13.4 - - - -
244K GLN 3.1 6.8 + - - +
258K VAL* 3.6 27.1 - - - +
274K PHE 3.2 16.6 + - - -
275K PHE* 3.8 1.8 - - - -
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Residues in contact with GLN 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J LYS 3.7 9.3 + - - -
225J SER* 3.6 13.0 + - - -
243J TYR 4.0 0.3 - - - +
244J GLN* 3.1 40.8 + - - +
154K TRP* 4.6 0.2 - - - -
186K SER* 1.3 75.1 + - - +
188K THR* 1.3 63.6 + - - +
241K SER* 4.3 6.2 - - - +
242K ILE 3.1 13.7 - - - +
243K TYR* 3.6 17.4 + - + +
272K ALA 3.6 11.9 - - - +
273K SER* 3.0 6.1 - - - -
274K PHE* 2.8 81.9 + - + +
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Residues in contact with THR 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K ILE* 4.1 8.7 - - + -
154K TRP* 4.9 2.9 - - + -
186K SER* 3.7 10.8 - - - +
187K GLN* 1.3 79.2 - - - +
189K TYR* 1.3 60.5 + - - +
190K PHE* 3.2 25.9 - - - -
208K GLN* 3.4 25.9 + - - +
242K ILE* 2.9 28.4 + - - +
258K VAL* 4.1 6.3 - - + -
260K VAL* 3.9 23.8 - - + -
266K ILE* 4.4 7.0 - - - -
272K ALA 4.4 0.7 - - - -
273K SER* 3.9 5.8 - - - -
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Residues in contact with TYR 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H GLU* 2.6 31.4 + - - -
224J LYS* 3.9 15.0 - - + -
226J ALA* 3.8 12.2 - - + +
188K THR* 1.3 72.3 - - - +
190K PHE* 1.3 71.8 - - - +
191K ARG* 3.5 17.2 + - + -
239K LEU* 2.9 29.8 - - + +
240K TYR 4.1 1.6 - - - -
241K SER* 3.5 24.7 - - - +
266K ILE* 3.4 5.4 - - - +
267K ASP* 2.9 52.4 + - + +
272K ALA* 3.4 36.5 + - + +
273K SER* 3.3 12.7 + - - +
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Residues in contact with PHE 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K THR* 3.2 26.0 - - - -
189K TYR* 1.3 71.6 - - - +
191K ARG* 1.3 59.6 + - - +
192K PHE* 4.3 2.9 - - + -
206K MET* 3.4 45.5 - - + -
207K VAL 3.9 21.8 - - - -
238K GLY 3.6 1.2 - - - +
239K LEU* 3.6 2.3 - - - -
240K TYR* 2.9 47.0 + - - +
242K ILE* 4.1 16.6 - - + -
260K VAL* 4.0 6.7 - - + -
261K THR 3.1 27.8 - - - -
262K ASN* 4.0 9.2 - - + -
265K LEU* 3.6 11.7 - - + +
266K ILE* 3.2 23.6 - - + -
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Residues in contact with ARG 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H ASP* 2.4 51.2 + - - +
98H GLU* 3.4 17.2 + - - -
99H MET* 3.0 37.1 - - + +
189K TYR* 3.5 28.0 + - + -
190K PHE* 1.3 74.3 - - - +
192K PHE* 1.3 61.5 + - - +
238K GLY 3.3 2.9 - - - -
239K LEU* 3.4 10.1 - - + -
265K LEU* 3.0 19.9 + - - +
267K ASP* 3.2 36.6 + - + +
269K ASP* 5.3 0.8 + - - -
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Residues in contact with PHE 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H MET* 4.1 5.2 - - - +
190K PHE 4.3 2.9 - - - -
191K ARG* 1.3 83.0 - - - +
193K GLN* 1.3 59.2 + - - +
194K GLU* 3.2 44.4 + - + +
204K LYS* 3.7 24.9 - - + -
206K MET* 3.8 16.6 - - + -
229K SER* 4.3 4.7 - - - -
237K TYR* 3.2 5.7 - - - +
238K GLY* 2.8 41.5 + - - +
240K TYR* 3.6 39.3 - + - -
265K LEU* 3.8 33.4 - - + -
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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