Contacts of the helix formed by residues 245 - 255 (chain D) in PDB entry 5MKE
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 ASN 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A VAL* 5.0 14.5 - - - +
383A ILE* 5.7 9.9 - - + -
446A PRO* 5.0 12.5 - - + +
447A ALA* 4.9 5.7 - - - +
448A THR* 3.2 30.6 + - + +
628A THR* 6.2 0.2 - - - -
243D SER* 3.8 13.1 + - - +
244D SER* 1.3 82.1 + - - +
246D VAL* 1.3 89.4 + - - +
247D TYR 3.1 0.7 - - - -
248D TYR* 3.0 19.9 + - + +
249D TYR* 2.9 17.7 + - - +
433D ILE* 4.7 12.9 - - - +
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Residues in contact with VAL 246 (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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620A GLY* 4.3 5.4 - - - +
241D MET 5.1 0.2 - - - +
242D MET* 4.1 20.2 - - + -
243D SER* 3.1 29.4 - - - +
244D SER 2.8 1.0 + - - -
245D ASN* 1.3 88.1 + - - +
247D TYR* 1.3 63.3 + - - +
249D TYR* 3.0 21.1 + - + +
250D THR* 3.0 13.3 + - + +
433D ILE* 4.3 18.6 - - + -
435D LEU* 4.3 18.8 - - + -
459D PRO* 4.7 18.2 - - + -
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Residues in contact with TYR 247 (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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620A GLY* 3.3 13.2 + - - +
621A THR 3.9 14.4 - - - -
623A VAL* 3.1 27.6 - - + -
624A ASP* 2.5 35.4 + - - +
625A ASP 4.1 0.9 + - - -
626A PHE 3.3 25.1 - - - -
627A SER* 3.0 36.1 - - - +
628A THR* 3.9 4.7 - - + -
631A GLU* 5.6 2.5 - - - -
244D SER 3.3 3.7 + - - +
246D VAL* 1.3 74.0 - - - +
248D TYR* 1.3 100.8 + + - +
250D THR* 2.2 31.6 + - - -
251D ARG* 3.0 19.0 + - + -
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Residues in contact with TYR 248 (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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382A ILE* 4.5 9.2 - - + +
383A ILE* 5.2 11.9 - - + -
446A PRO* 5.1 11.2 - - + -
448A THR* 4.9 1.8 - - - +
451A VAL 6.3 0.2 - - - -
452A ILE* 3.1 44.6 - - + +
628A THR* 3.4 29.8 - - + +
631A GLU* 5.3 2.9 + - - -
245D ASN* 3.0 20.0 + - + +
247D TYR* 1.3 93.1 - + - +
249D TYR* 1.3 55.9 + - - +
250D THR 2.6 13.7 + - - -
251D ARG* 2.7 53.1 + - + -
252D MET* 2.8 28.1 + - + -
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Residues in contact with TYR 249 (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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448A THR* 3.4 35.9 - - + -
245D ASN 2.9 6.3 + - - -
246D VAL* 3.0 20.4 + - + +
248D TYR* 1.3 74.3 - - - +
250D THR* 1.3 57.6 - - + +
252D MET* 3.5 12.7 - - + +
253D MET* 3.1 49.1 - - + +
313D ASN* 3.1 24.8 + - - -
429D TYR* 3.8 2.3 + - - -
430D ASN* 3.1 49.2 + - + +
433D ILE* 5.4 1.1 - - + -
435D LEU* 3.8 23.2 + - + -
437D CYS* 4.4 16.8 - - + +
459D PRO* 5.4 2.9 - - + -
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Residues in contact with THR 250 (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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620A GLY 3.2 24.0 - - - +
621A THR* 3.6 4.8 + - - -
622A GLN* 3.1 35.7 + - - +
246D VAL* 3.5 8.7 - - + +
247D TYR* 2.2 24.4 + - - -
248D TYR 2.6 5.3 + - - -
249D TYR* 1.3 73.9 - - + +
251D ARG* 1.3 60.3 + - - +
253D MET* 2.8 6.1 + - - +
254D SER* 2.7 36.3 + - - -
457D PHE* 5.6 5.3 - - + -
459D PRO* 5.2 15.7 - - + -
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Residues in contact with ARG 251 (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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451A VAL 5.7 2.0 + - - -
452A ILE* 5.2 4.6 - - - +
622A GLN* 4.0 14.6 - - + +
623A VAL 5.1 0.2 - - - +
624A ASP* 2.8 24.1 + - - +
247D TYR* 3.0 39.5 - - + +
248D TYR* 2.7 49.6 + - - +
250D THR* 1.3 84.0 + - - +
252D MET* 1.3 68.5 + - - +
254D SER* 2.5 39.2 + - - +
255D GLN* 3.0 33.7 + - - +
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Residues in contact with MET 252 (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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446A PRO* 5.5 1.3 - - - -
448A THR* 2.4 55.0 - - - +
449A GLY* 3.3 4.9 - - - +
450A GLY* 3.1 37.0 - - - +
451A VAL 4.9 2.9 - - - +
248D TYR* 2.8 40.5 + - + +
249D TYR* 3.5 18.2 - - + -
251D ARG* 1.3 79.3 - - + +
253D MET* 1.3 63.0 + - + +
255D GLN* 5.5 2.2 - - - -
256D LEU* 3.3 31.3 - - - +
313D ASN* 5.1 1.8 - - - +
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Residues in contact with MET 253 (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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249D TYR* 3.1 54.1 - - + +
250D THR 2.8 3.9 + - - +
252D MET* 1.3 86.9 - - + +
254D SER* 1.3 64.4 + - - +
256D LEU* 4.5 6.7 - - - +
257D PHE* 3.7 23.0 - - + -
309D ILE* 5.4 9.2 - - + -
310D PHE* 6.5 0.9 - - + -
313D ASN* 3.3 26.2 - - + +
428D VAL* 3.8 29.2 - - + -
429D TYR 5.1 0.7 - - - +
437D CYS* 5.4 7.0 - - + -
457D PHE* 5.4 1.4 - - - -
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Residues in contact with SER 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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622A GLN* 2.8 45.0 + - - -
250D THR 2.7 9.4 + - - -
251D ARG* 2.5 22.2 + - - +
253D MET* 1.3 73.5 - - - +
255D GLN* 1.3 66.8 + - - +
256D LEU 2.5 5.6 + - - -
257D PHE* 2.4 37.4 + - - +
258D LEU* 4.3 4.3 - - - -
457D PHE* 3.7 21.1 - - - -
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Residues in contact with GLN 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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274A SER* 4.4 14.5 + - - -
622A GLN* 4.9 5.0 + - - +
251D ARG* 3.0 36.3 + - - +
252D MET* 5.5 1.6 - - - -
254D SER* 1.3 84.4 + - - +
256D LEU* 1.3 57.8 + - + +
257D PHE 2.8 5.1 + - - +
258D LEU* 4.0 9.2 - - + +
259D ASP* 4.0 27.6 - - + +
260D THR* 2.7 33.6 + - - -
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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