Contacts of the strand formed by residues 184 - 192 (chain D) in PDB entry 2VKM
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 TYR 184 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ILE* 4.1 4.4 - - + +
180D ASP 3.8 3.8 - - - -
181D HIS* 2.7 68.2 + - + +
182D SER 3.4 2.3 - - - +
183D LEU* 1.3 80.7 - - - +
185D THR* 1.3 69.5 + - - +
186D GLY 3.4 24.0 - - - -
187D SER* 4.7 0.7 - - - -
188D LEU* 4.0 28.1 - - + +
342D TYR* 3.4 32.3 - + + -
355D ALA* 3.5 25.1 - - + -
356D VAL 3.1 16.4 - - - +
358D ALA* 3.9 3.7 - - - +
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Residues in contact with THR 185 (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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184D TYR* 1.3 85.1 - - - +
186D GLY* 1.3 70.5 + - - +
187D SER 3.8 0.2 + - - -
355D ALA* 4.2 0.3 - - - +
356D VAL* 3.1 43.5 + - - +
358D ALA* 4.8 15.0 - - + -
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Residues in contact with GLY 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D TYR* 3.4 15.6 - - - -
185D THR* 1.3 81.5 - - - +
187D SER* 1.3 58.6 + - - -
356D VAL* 6.1 1.1 - - - -
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Residues in contact with SER 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D TYR* 4.6 2.5 - - - -
185D THR 4.5 0.2 - - - +
186D GLY* 1.3 73.4 - - - -
188D LEU* 1.3 65.0 + - - +
189D TRP* 3.9 20.9 + - - -
354D PHE 3.6 3.3 - - - +
355D ALA* 3.5 19.0 - - - +
370D VAL* 4.5 5.0 + - - +
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Residues in contact with LEU 188 (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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179D ILE* 4.2 13.0 - - + -
181D HIS* 6.2 0.2 - - + -
184D TYR* 4.0 26.5 - - + +
187D SER* 1.3 76.0 - - - +
189D TRP* 1.3 62.8 + - - +
190D TYR* 3.6 37.1 - - + +
342D TYR* 4.4 6.1 - - + +
344D VAL* 3.9 26.9 - - + -
353D GLY* 3.9 2.5 - - - +
354D PHE* 3.3 20.9 - - - +
355D ALA* 3.6 22.7 - - + +
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Residues in contact with TRP 189 (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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187D SER* 4.1 20.4 + - - -
188D LEU* 1.3 78.1 - - - +
190D TYR* 1.3 63.0 + - - +
289D GLY* 5.9 3.1 - - - -
294D GLN* 4.0 17.9 - - + -
295D SER 4.8 1.6 - - - -
296D PHE* 3.5 54.6 - + + -
352D ILE 3.7 0.9 - - - +
353D GLY* 3.2 0.7 - - - -
354D PHE 2.8 30.4 + - - -
370D VAL* 3.6 29.6 + - + -
371D GLU* 4.6 0.2 - - - +
372D GLY 3.3 28.1 - - - +
373D PRO* 3.4 32.1 - - + -
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Residues in contact with TYR 190 (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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179D ILE* 3.9 14.7 - - - +
188D LEU* 3.6 40.5 - - + +
189D TRP* 1.3 78.7 - - - +
191D THR* 1.3 60.1 + - - +
289D GLY* 3.7 0.9 - - - -
290D GLU* 3.6 41.4 + - + +
296D PHE* 3.2 13.9 - - - -
344D VAL* 4.2 11.8 - - + +
346D ASP* 4.5 3.7 + - + -
351D ARG* 3.4 56.8 + - + -
352D ILE 3.3 2.7 - - - -
353D GLY* 3.3 33.4 - - - -
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Residues in contact with THR 191 (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 TYR* 1.3 75.0 - - - +
192D PRO* 1.3 69.7 + - - +
201D VAL* 3.8 30.1 - - + +
202D ILE 4.6 2.9 + - - -
287D LEU* 3.8 9.8 - - + +
288D MET* 2.7 28.4 + - - +
290D GLU* 4.9 0.4 - - - -
296D PHE* 3.8 11.6 - - - -
351D ARG* 3.4 5.3 - - - +
352D ILE* 2.9 41.9 + - + +
354D PHE* 4.0 16.2 - - + -
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Residues in contact with PRO 192 (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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191D THR* 1.3 98.1 + - - +
193D ILE* 1.3 64.6 + - - +
194D ARG* 3.2 8.7 + - - +
200D GLU 3.7 4.3 - - - +
201D VAL* 4.0 9.9 - - - +
202D ILE* 4.8 1.0 + - - +
288D MET* 3.2 26.9 - - + +
289D GLY 3.5 20.9 - - - +
290D GLU* 4.4 11.0 - - + +
350D LYS 4.0 7.2 - - - +
351D ARG* 4.4 2.5 - - + -
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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