Contacts of the helix formed by residues 286 - 292 (chain D) in PDB entry 5MKV
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 ASP 286 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D THR* 1.3 83.8 + - - +
287D GLY* 1.3 58.5 + - - +
288D SER* 2.7 35.9 + - - -
289D HIS* 3.3 21.0 + - - -
301D PHE* 4.0 8.7 - - - -
307D LEU* 3.7 10.3 - - - +
308D SER 3.5 13.0 - - - +
309D PRO 4.7 0.7 - - - +
310D ASP 4.2 2.7 - - - +
311D PRO* 3.7 36.9 - - + +
313D THR* 5.8 0.2 - - - -
314D PRO* 4.8 5.0 - - + +
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Residues in contact with GLY 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ASP* 1.3 70.2 - - - +
288D SER* 1.3 64.4 + - - +
289D HIS 2.9 4.0 + - - -
290D TYR* 3.1 27.7 + - - -
291D TRP* 3.4 9.9 - - - -
301D PHE* 5.3 2.0 - - - -
307D LEU* 3.5 27.7 - - - +
308D SER 2.8 15.1 + - - -
309D PRO* 4.0 6.7 - - - -
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Residues in contact with SER 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ASP* 2.7 24.9 + - - -
287D GLY* 1.3 77.0 - - - +
289D HIS* 1.3 76.3 + - - +
290D TYR 3.3 1.2 + - - -
291D TRP* 3.3 26.6 + - - +
292D SER 4.4 0.9 + - - -
309D PRO* 4.1 11.5 - - - +
311D PRO* 6.3 0.9 - - - -
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Residues in contact with HIS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D THR* 3.7 12.7 + - - -
286D ASP* 3.3 24.2 + - - -
287D GLY 2.9 1.2 - - - -
288D SER* 1.3 87.5 + - - +
290D TYR* 1.3 59.6 + - - +
291D TRP 3.0 5.2 - - - -
292D SER* 3.0 24.0 + - - +
297D LYS* 3.9 25.9 + - - -
298D ALA* 3.5 10.2 - - - +
301D PHE* 3.6 41.0 - + + -
433D ILE 5.4 0.6 + - - -
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Residues in contact with TYR 290 (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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496B ARG* 3.0 19.4 + - - -
220D PRO 4.0 13.7 - - - -
221D GLU* 3.6 16.4 + - - +
223D HIS* 4.7 3.8 - + - -
224D VAL* 3.5 37.2 - - + -
287D GLY* 3.1 30.5 + - - +
289D HIS* 1.3 77.5 - - - +
291D TRP* 1.3 61.9 + - + +
292D SER 3.4 0.2 - - - -
298D ALA* 3.5 19.9 - - - +
301D PHE* 2.7 46.5 + - + +
302D VAL* 3.6 12.8 - - + -
303D THR 4.1 2.9 + - - -
306D PRO* 3.5 11.8 - - + +
307D LEU* 3.1 41.2 + - + +
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Residues in contact with TRP 291 (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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492B ARG 4.9 7.8 + - - -
494B VAL* 3.5 36.3 - - + +
496B ARG* 3.9 0.9 - - - -
221D GLU* 3.6 18.1 - - + +
224D VAL* 3.5 25.1 - - + -
225D LEU* 3.9 32.5 - - + +
287D GLY 3.4 26.2 - - - -
288D SER* 3.3 15.9 + - - +
289D HIS 3.0 1.2 - - - -
290D TYR* 1.3 78.6 - - + +
292D SER* 1.3 66.7 + - - +
293D LYS* 3.4 3.1 + - - +
309D PRO* 3.9 24.5 - - + -
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Residues in contact with SER 292 (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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494B VAL* 4.2 0.5 - - - +
496B ARG* 2.9 28.4 + - - -
288D SER 4.4 0.2 + - - -
289D HIS* 3.0 22.2 + - - +
290D TYR 3.4 0.8 - - - -
291D TRP* 1.3 77.0 - - - +
293D LYS* 1.3 62.9 + - - +
294D ASN* 3.2 24.5 + - - +
297D LYS* 3.7 29.9 + - - +
298D ALA* 4.3 1.3 - - - -
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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