Contacts of the strand formed by residues 206 - 215 (chain D) in PDB entry 3K9X
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 THR 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C ASP 5.5 0.5 + - - -
138C GLN* 4.3 14.1 + - - +
155C TYR* 4.3 1.8 - - - +
172C CYS 3.7 11.7 - - - +
173C GLY* 3.5 3.6 - - - +
174C LYS* 3.0 22.5 + - - +
122D CYS* 3.6 29.4 - - - -
202D ARG* 4.3 0.4 - - - +
203D PHE 2.9 33.6 + - - +
204D LYS 3.5 7.1 + - - -
205D ASP* 1.3 78.4 - - - +
207D TYR* 1.3 63.9 + - - +
208D PHE* 3.4 24.3 - - + -
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Residues in contact with TYR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY* 2.9 24.5 + - - -
175C GLN* 3.6 34.6 + - + -
29D TRP* 3.6 32.1 - + + -
121D ALA* 4.1 1.2 - - + -
122D CYS* 3.1 24.3 + - - +
137D ILE* 3.8 19.8 - - + +
200D VAL* 3.7 26.5 - - + -
201D THR 3.7 1.6 - - - -
202D ARG* 2.8 64.3 + - + -
205D ASP 4.7 4.9 - - - -
206D THR* 1.3 75.1 - - - +
208D PHE* 1.3 61.3 + - - +
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLN* 4.5 15.5 - - + -
139C PHE* 3.5 24.7 - + - -
152C ALA* 4.4 2.7 - - + -
122D CYS* 3.2 35.4 - - + +
124D PRO* 4.0 18.8 - - + -
127D TRP* 3.7 20.0 - + - -
131D LEU* 3.5 31.9 - + + -
200D VAL* 3.2 5.5 - - - -
201D THR 2.9 37.2 + - - +
203D PHE* 4.1 9.4 - + + -
206D THR* 3.4 39.0 - - + -
207D TYR* 1.3 73.4 - - - +
209D VAL* 1.3 63.7 + - - +
210D THR* 3.3 1.2 + - - +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 4.2 10.1 - - + +
47D LEU* 4.0 20.2 - - + -
53D LEU* 3.8 26.7 - - + -
121D ALA* 3.6 23.6 - - + -
122D CYS 2.9 16.0 + - - +
123D LEU* 4.2 9.9 - - + -
124D PRO* 3.5 22.5 - - - +
198D PRO* 5.8 0.2 - - + -
199D HIS 3.8 5.4 - - - +
200D VAL* 4.2 3.3 - - + +
207D TYR 4.4 0.4 + - - -
208D PHE* 1.3 69.1 - - - +
210D THR* 1.4 62.3 + - - +
211D GLY 4.0 9.9 - - - +
231D VAL* 3.7 21.2 - - + +
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Residues in contact with THR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PRO* 5.3 0.9 - - + -
128D ALA* 5.5 1.8 - - + -
131D MET* 3.7 41.7 + - + +
162D TYR* 3.4 14.4 - - - +
181D PHE* 3.4 11.7 - - - -
199D HIS* 2.8 25.2 + - - -
201D THR* 2.8 38.8 + - - +
208D PHE 3.9 0.7 - - - +
209D VAL* 1.4 77.7 - - - +
211D GLY* 1.3 58.7 + - - +
231D VAL* 3.3 23.0 + - - +
232D THR* 4.8 3.4 + - + +
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Residues in contact with GLY 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D THR* 5.3 0.3 + - - -
53D LEU* 5.1 0.2 - - - +
181D PHE* 4.1 6.7 - - - -
197D GLY 4.0 1.2 - - - +
198D PRO* 4.0 0.9 - - - +
199D HIS* 3.0 39.0 + - - +
209D VAL* 4.0 8.0 - - - +
210D THR* 1.3 79.8 + - - +
212D ILE* 1.3 67.5 + - - +
228D TYR* 4.4 0.7 - - - -
229D THR 3.2 12.3 - - - -
231D VAL* 3.6 4.4 - - - +
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.6 28.7 - - + -
54D THR 3.6 10.1 - - - +
55D ALA* 3.8 14.6 - - + +
102D ASP 4.1 4.0 - - - +
103D ILE* 3.5 42.2 - - + -
196D GLY* 3.6 32.8 - - - +
197D GLY 3.5 3.6 - - - -
211D GLY* 1.3 78.1 - - - +
213D VAL* 1.3 70.6 + - - +
214D SER 3.2 0.9 + - - -
228D TYR* 3.2 5.3 - - - -
229D THR* 2.8 39.5 + - - +
231D VAL* 3.8 6.1 - - + -
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D MBM 3.0 34.3 - - + +
55D ALA* 4.0 3.3 - - - +
138D VAL* 3.3 33.0 - - + -
139D SER 4.7 0.7 - - - +
190D ALA* 4.1 0.7 - - + -
194D ASP* 3.3 37.7 - - + +
195D SER* 3.6 10.1 - - - +
196D GLY 2.9 23.6 + - - +
197D GLY 3.1 19.4 + - - +
198D PRO 4.4 0.7 - - - +
212D ILE* 1.3 74.2 - - - +
214D SER* 1.3 58.1 + - - +
228D TYR* 3.8 13.3 - - + -
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Residues in contact with SER 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D MBM 4.3 3.5 - - - +
57D HIS* 3.1 23.4 + - - -
99D TYR* 3.9 3.1 + - - +
102D ASP* 2.5 32.9 + - - +
180D MET* 6.0 1.4 - - - +
195D SER* 3.7 5.6 + - - -
212D ILE 3.2 2.2 + - - -
213D VAL* 1.3 76.5 - - - +
215D TRP* 1.3 82.5 + - - +
227D ILE* 3.0 16.1 + - - -
228D TYR 4.3 0.7 - - - -
229D THR* 3.7 20.6 - - - -
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Residues in contact with TRP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D MBM 3.1 67.6 + + + +
98D THR 4.2 1.2 + - - -
99D TYR* 3.8 15.3 - - + -
172D SER* 3.6 22.4 - - - -
174D PHE* 3.8 28.7 - + + -
175D ILE 3.9 10.8 - - - -
176D ILE* 3.6 21.8 - - + -
180D MET* 3.7 17.0 - - + +
214D SER* 1.3 104.7 - - - +
216D GLY* 1.3 75.8 + - - +
217D GLU* 4.2 12.8 - - + -
227D ILE* 2.8 57.3 + - + +
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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