Contacts of the strand formed by residues 253 - 259 (chain D) in PDB entry 3K75
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 ARG 253 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ASP 4.3 3.3 + - - -
146D PHE* 3.6 6.3 - - - -
148D LYS* 4.0 18.4 + - - +
149D ARG 3.1 20.4 + - - -
150D ILE* 3.6 37.9 - - + +
151D PRO* 3.4 11.1 - - - +
154D GLU* 2.9 40.8 + - - +
158D MET* 4.4 14.6 - - + -
238D VAL* 3.5 4.7 - - - +
239D CYS* 3.0 43.6 + - - +
240D GLN* 5.5 2.0 - - - -
241D LEU* 5.9 1.3 - - + +
251D PRO* 3.6 34.5 + - - +
252D HIS* 1.3 82.8 - - - +
254D ARG* 1.3 65.6 + - - +
255D ILE 3.5 0.3 + - - -
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Residues in contact with ARG 254 (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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104D THR* 3.9 12.5 + - - -
146D PHE* 3.7 46.6 - - + +
150D ILE* 5.1 1.2 - - - +
189D GLY 5.0 3.5 + - - +
190D ASP* 3.6 22.9 + - + +
191D MET* 3.2 25.6 + - - +
228D LEU* 3.4 22.5 - - - +
236D MET* 3.1 23.2 - - - +
237D GLY 3.4 13.7 + - - +
239D CYS* 5.2 0.2 - - - -
253D ARG* 1.3 75.5 - - - +
255D ILE* 1.3 87.7 + - - +
256D ASP* 3.1 23.1 + - - -
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Residues in contact with ILE 255 (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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162D VAL* 4.5 5.4 - - + -
190D ASP* 5.7 0.2 - - - -
191D MET* 3.6 23.1 - - + +
193D VAL* 4.7 1.8 - - + -
218D LEU* 5.3 0.9 - - + -
223D PHE* 3.8 30.1 - - + -
224D ILE* 4.8 6.1 - - + -
235D PHE* 3.9 15.2 - - + +
236D MET* 3.8 0.7 - - - -
237D GLY 3.0 45.1 + - - +
238D VAL 4.0 9.4 - - - +
239D CYS* 4.0 14.8 - - + -
253D ARG 3.5 0.4 + - - -
254D ARG* 1.3 80.4 + - - +
256D ASP* 1.3 74.0 + - - +
257D ILE* 4.2 17.9 - - + -
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Residues in contact with ASP 256 (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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190D ASP* 4.8 9.0 + - - +
191D MET 3.0 9.8 + - - +
192D ASP* 3.5 22.9 - - - +
193D VAL* 2.9 27.5 + - - +
234D LYS* 4.4 10.7 + - + +
235D PHE 3.6 4.9 - - - +
236D MET* 3.7 14.5 - - - +
254D ARG* 3.1 30.9 + - - -
255D ILE* 1.3 79.5 - - - +
257D ILE* 1.3 68.8 + - - +
258D ARG* 4.4 15.2 + - + -
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Residues in contact with ILE 257 (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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162D VAL* 5.8 1.6 - - + -
193D VAL* 3.4 20.0 - - + -
195D LEU* 4.4 18.4 - - + -
211D LEU* 3.3 23.6 - - + +
214D VAL* 4.9 5.6 - - + -
215D VAL* 4.9 6.5 - - + -
218D LEU* 4.0 27.8 - - + -
224D ILE* 4.6 4.9 - - + -
233D THR 3.9 0.5 - - - +
234D LYS* 3.3 2.1 - - - -
235D PHE* 2.8 57.5 + - + +
255D ILE* 4.2 17.9 - - + -
256D ASP* 1.3 80.2 - - - +
258D ARG* 1.3 61.9 + - - +
259D LEU 3.8 0.5 + - - -
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Residues in contact with ARG 258 (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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192D ASP* 4.1 16.4 + - - +
193D VAL 2.9 8.4 + - - +
194D LEU* 3.5 20.3 - - + -
195D LEU* 2.6 36.4 + - - +
233D THR 3.6 4.9 - - - +
234D LYS* 3.4 48.0 - - + +
256D ASP* 4.4 10.2 + - + -
257D ILE* 1.3 76.5 - - - +
259D LEU* 1.3 55.8 + - - +
260D ILE* 3.8 11.8 + - + +
272D PHE* 3.6 50.1 - - - -
295D GLU* 5.2 2.2 + - - -
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Residues in contact with LEU 259 (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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173D TYR* 5.4 0.7 - - + -
195D LEU* 3.7 38.8 - - + +
196D THR* 4.3 7.4 - - - +
197D HIS* 5.9 0.2 - - + -
200D PHE* 3.8 28.1 - - + -
207D GLN 3.7 26.2 - - - +
210D LEU* 4.0 15.0 - - + -
211D LEU* 3.9 24.8 - - + +
232D GLU 4.5 7.2 - - - +
233D THR* 2.5 35.5 + - + +
257D ILE 3.8 1.2 + - - -
258D ARG* 1.3 73.0 - - - +
260D ILE* 1.3 64.0 - - - +
261D PRO* 4.5 2.1 - - - +
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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