Contacts of the helix formed by residues 375 - 384 (chain A) in PDB entry 5M8L
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 SER 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ASP* 5.5 2.2 - - - -
358A THR 3.7 6.1 + - - -
361A GLY* 3.0 28.2 + - - -
363A SER 2.5 29.2 + - - -
364A ASP* 4.1 2.9 - - - -
365A PRO* 4.1 22.9 - - - -
373A VAL* 4.3 3.8 - - - -
374A ARG* 1.3 75.2 - - - +
376A LEU* 1.3 73.4 + - - +
378A ASN 3.1 0.3 + - - -
379A LEU* 3.1 15.4 + - - -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PHE* 4.0 12.8 - - + -
328A PRO* 3.5 25.2 - - + +
332A ASP* 3.8 34.5 - - + +
333A VAL* 3.7 30.5 - - + -
336A CYS* 3.9 19.7 - - + -
358A THR* 3.5 22.2 - - + +
359A VAL* 3.7 18.6 - - + +
365A PRO* 4.6 6.1 - - + -
375A SER* 1.3 77.3 - - - +
377A HIS* 1.3 67.5 + - - +
379A LEU* 2.9 3.5 + - - +
380A ALA* 2.9 23.6 + - - +
406A PHE* 5.9 0.4 - - + -
410A VAL* 6.1 1.3 - - + -
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A HIS* 4.9 6.3 - + - -
220A PHE* 3.5 27.1 - + + -
251A PHE* 4.2 12.4 - - - -
359A VAL* 3.1 19.7 + - + +
360A GLU* 2.9 19.1 + - + -
375A SER 3.2 0.8 + - - -
376A LEU* 1.3 79.7 - - - +
378A ASN* 1.3 74.2 + - - +
380A ALA* 3.5 2.8 + - - +
381A HIS* 3.1 29.9 + + - -
403A LEU* 3.6 15.9 - - + +
404A HIS* 3.2 16.7 + + - -
407A THR* 3.9 14.8 - - + +
513A ZN 2.0 37.3 - - - -
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Residues in contact with ASN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A GLU* 3.0 28.8 + - - +
361A GLY 3.3 23.1 + - - +
362A TYR* 3.4 37.0 + - - -
374A ARG* 4.2 14.4 - - + +
375A SER 3.1 6.6 + - - +
377A HIS* 1.3 90.5 + - - +
379A LEU* 1.3 63.0 + - - +
381A HIS* 3.2 7.7 + - - +
382A LEU* 3.1 29.8 + - + +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A MET 3.4 24.9 - - - +
324A VAL* 3.7 18.2 - - + -
326A ARG 3.5 22.9 - - - +
327A LEU* 3.8 2.2 - - - +
328A PRO* 3.6 30.1 - - + -
332A ASP* 5.4 1.3 - - - +
374A ARG* 3.7 20.2 - - - +
375A SER* 3.1 18.9 + - - +
376A LEU 2.9 9.9 + - - +
378A ASN* 1.3 77.6 - - - +
380A ALA* 1.3 55.8 + - - +
382A LEU* 3.3 2.1 + - - +
383A PHE* 2.9 29.6 + - + +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TRP* 4.6 4.4 - - + -
251A PHE* 3.7 36.3 - - + -
327A LEU* 4.3 10.5 - - + -
328A PRO* 4.6 1.0 - - + +
376A LEU 2.9 14.5 + - - +
377A HIS 3.8 3.6 - - - +
378A ASN 3.2 0.2 - - - -
379A LEU* 1.3 78.5 - - - +
381A HIS* 1.3 60.9 + - - +
383A PHE* 3.5 12.5 - - - +
384A LEU* 3.6 13.5 - - - +
403A LEU* 3.8 20.9 - - + +
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A HIS* 3.2 30.7 + + - -
378A ASN* 3.2 10.6 + - - +
380A ALA* 1.3 78.3 - - - +
382A LEU* 1.3 64.4 + - + +
384A LEU* 3.2 21.7 + - - +
385A ASN 4.2 0.3 + - - -
388A GLY 2.6 24.8 + - - +
389A GLY* 3.5 17.9 + - - -
394A SER* 3.7 19.6 - - - -
400A PHE* 3.7 16.2 - + + -
403A LEU* 3.8 18.1 - - + +
404A HIS* 3.6 1.8 + - - -
513A ZN 2.1 37.1 - - - -
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ASN* 4.9 1.8 + - - +
321A ARG* 4.0 21.8 - - - +
324A VAL* 3.7 42.6 - - + +
374A ARG* 3.9 29.8 - - + +
378A ASN* 3.1 18.1 + - + +
379A LEU 4.1 1.1 - - - +
381A HIS* 1.3 77.7 - - + +
383A PHE* 1.3 65.6 + - - +
384A LEU 3.0 1.8 - - - -
385A ASN* 3.1 17.4 + - - +
389A GLY* 4.1 22.7 - - - +
1I NAG 5.4 1.3 - - - +
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Residues in contact with PHE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TRP* 4.9 2.2 - + - -
255A LYS 4.2 0.7 - - - -
256A ASN 3.7 18.6 - - - -
257A VAL* 3.8 20.4 - - - -
258A CYS* 4.1 5.6 - - + -
314A ASN 4.0 0.7 - - - +
315A PRO* 3.4 19.0 - - + +
316A ALA* 3.0 43.0 + - + -
324A VAL 3.4 11.7 + - - +
325A GLN 3.6 21.8 - - - -
326A ARG* 3.8 24.0 - - - +
327A LEU* 3.4 33.9 - - + -
379A LEU 2.9 19.0 + - - +
380A ALA 3.5 7.4 - - - +
381A HIS 3.2 0.2 - - - -
382A LEU* 1.3 77.7 - - - +
384A LEU* 1.3 68.9 + - + +
385A ASN* 3.3 1.7 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TRP* 4.7 7.2 - - + -
258A CYS* 5.1 2.2 - - - -
313A ARG* 3.8 16.0 - - + -
314A ASN 2.8 25.7 + - - -
315A PRO* 4.4 9.2 - - + -
380A ALA 3.6 15.0 - - - +
381A HIS* 3.2 12.8 + - - +
382A LEU 3.0 1.0 - - - -
383A PHE* 1.3 87.1 - - + +
385A ASN* 1.3 67.3 + - - +
386A GLY* 3.3 1.0 + - - +
388A GLY* 4.0 29.2 - - - +
397A ASP* 4.2 9.6 - - + +
399A ILE* 4.0 42.6 - - + -
400A PHE 5.6 1.3 - - - +
403A LEU* 4.8 5.6 - - + -
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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