Contacts of the strand formed by residues 205 - 213 (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 GLN 205 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95I ASP 3.4 10.8 + - - +
96I SER* 3.6 16.8 - - - -
98I GLU* 3.2 16.8 + - - +
99I MET* 3.1 43.2 + - - +
101I ARG* 3.6 10.4 - - - +
203K ASP* 5.1 0.4 - - - +
204K LYS* 1.3 73.5 - - - +
206K MET* 1.3 54.6 + - - +
207K VAL* 3.5 6.4 + - + +
227K ARG 3.9 4.7 - - - -
261K THR* 2.6 26.9 + - - -
262K ASN* 3.1 10.5 + - - +
237L TYR* 2.8 46.3 + - + +
239L LEU* 4.2 9.0 - - + -
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Residues in contact with MET 206 (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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190K PHE* 3.4 44.2 - - + -
192K PHE* 3.8 12.1 - - + -
204K LYS* 3.8 13.4 - - + +
205K GLN* 1.3 69.3 - - - +
207K VAL* 1.3 62.1 + - - +
226K ALA* 3.4 0.7 - - - -
227K ARG* 2.9 33.9 + - + +
228K ASN 3.8 6.1 - - - -
229K SER* 3.4 43.7 - - - +
240K TYR* 3.4 36.3 - - + -
242K ILE* 3.7 10.5 - - + +
261K THR* 3.8 3.4 - - - -
262K ASN* 4.4 9.0 - - + +
265K LEU* 5.3 1.1 - - + -
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Residues in contact with VAL 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I PRO* 5.2 0.9 - - + -
98I GLU* 3.5 30.5 - - + +
190K PHE* 3.9 6.1 - - - -
205K GLN* 3.7 15.5 - - + +
206K MET* 1.3 81.1 - - - +
208K GLN* 1.3 64.4 + - - +
209K TYR* 3.4 33.1 - - + +
224K LYS* 4.8 1.6 - - + -
225K SER 3.4 14.4 - - - +
226K ALA* 3.6 11.7 - - + -
260K VAL* 3.3 7.8 - - - +
261K THR* 3.2 41.7 + - + +
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Residues in contact with GLN 208 (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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186K SER* 3.1 48.4 + - - +
188K THR* 3.4 22.3 + - + +
207K VAL* 1.3 73.7 - - - +
209K TYR* 1.3 65.4 + - - +
210K ILE* 3.5 9.1 - - - +
224K LYS* 3.3 5.5 - - - +
225K SER* 2.9 32.6 + - - +
242K ILE* 3.2 30.9 - - + +
244K GLN* 3.2 27.7 + - - +
258K VAL* 4.0 15.0 - - + +
259K SER 3.8 2.5 - - - -
260K VAL* 4.5 1.3 - - + +
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Residues in contact with TYR 209 (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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97I PRO* 3.4 25.6 - - - +
98I GLU* 3.4 14.6 + - - +
147K LEU* 3.8 41.8 - - + +
207K VAL* 3.4 22.8 - - + +
208K GLN* 1.3 74.3 - - - +
210K ILE* 1.3 62.1 + - - +
211K TYR* 3.6 24.9 - + + -
221K LEU* 4.0 11.7 - - + -
223K MET 3.7 2.5 - - - -
224K LYS* 3.7 31.4 - - + -
258K VAL* 3.3 7.1 - - - +
259K SER* 2.7 44.9 + - - +
260K VAL* 4.5 0.9 - - - -
261K THR* 3.6 23.3 - - + -
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Residues in contact with ILE 210 (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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184K ILE* 4.1 20.9 - - + -
185K TYR* 4.2 6.3 - - - -
186K SER* 4.0 19.1 - - - +
208K GLN* 3.5 23.3 - - - +
209K TYR* 1.3 73.9 - - - +
211K TYR* 1.3 65.0 + - - +
221K LEU* 3.5 1.9 - - - +
222K LEU* 2.9 31.3 + - + +
223K MET* 3.1 32.4 + - + +
244K GLN* 3.4 27.8 - - + +
256K ILE* 5.5 1.1 - - + -
257K PHE 3.5 7.9 - - - +
258K VAL* 4.1 8.7 - - + -
275K PHE* 5.0 3.6 - - + -
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Residues in contact with TYR 211 (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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146K ALA* 3.5 19.1 - - + -
147K LEU* 2.6 50.3 + - - +
209K TYR* 3.6 23.8 - - + -
210K ILE* 1.3 79.0 - - - +
212K LYS* 1.3 63.9 + - - +
219K PRO* 3.7 17.0 - - + -
220K ILE 3.4 9.4 - - - -
221K LEU* 3.4 40.0 - - + +
222K LEU* 4.3 2.6 - - - +
256K ILE* 3.3 9.2 - - - +
257K PHE* 2.9 62.6 + + + +
259K SER* 4.2 4.0 - - - -
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Residues in contact with LYS 212 (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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57I LEU* 6.2 0.6 - - - +
211K TYR* 1.3 79.2 - - - +
213K TYR* 1.3 62.0 + - - +
214K THR* 4.2 15.5 + - + +
218K ASP 4.6 0.3 - - - +
219K PRO* 3.6 5.2 - - - +
220K ILE* 2.9 63.0 + - + +
222K LEU* 3.8 22.9 - - + +
248K PHE* 6.2 0.4 - - - +
249K GLU 4.0 18.4 + - - -
250K LEU* 4.3 8.0 - - + +
251K LYS* 5.9 1.6 - - - +
254K ASP* 4.1 21.6 + - - +
255K ARG 3.0 10.3 - - - +
256K ILE* 3.9 13.7 - - + -
257K PHE* 4.9 0.4 - - - -
160L GLY 5.2 8.1 + - - -
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Residues in contact with TYR 213 (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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146K ALA* 5.4 1.9 + - - +
150K LYS* 6.1 0.9 - - + -
173K GLU* 3.8 12.8 - - - -
212K LYS* 1.3 70.3 - - - +
214K THR* 1.3 61.9 + - - +
216K TYR 4.6 7.4 - - - -
217K PRO 4.4 8.1 - - - -
218K ASP 3.9 5.8 - - - -
219K PRO* 3.5 48.0 - - + +
253K ASN 4.4 1.7 - - - +
254K ASP* 3.2 6.7 - - - +
255K ARG* 2.6 84.3 + - - +
257K PHE* 3.4 31.5 - + - -
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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