Contacts of the helix formed by residues 375 - 392 (chain A) in PDB entry 5MQI
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 GLU 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A LEU* 3.5 34.4 - - + +
373A HIS 2.9 15.6 + - - +
374A ASP* 1.3 70.7 + - - +
376A THR* 1.3 66.0 + - - +
377A TYR 3.2 2.2 - - - -
378A TYR* 3.3 15.1 + - + +
379A MET* 3.3 18.0 + - + +
410A PHE* 5.7 1.8 - - + -
414A ASN* 3.9 13.8 - - - +
417A ASN* 5.5 0.9 + - - -
418A TYR* 2.5 41.6 + - - +
432A TRP* 5.6 0.5 - - - -
435A ARG* 5.0 3.9 - - - -
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Residues in contact with THR 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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173A LEU* 5.9 4.0 - - - +
374A ASP* 2.3 37.3 + - - +
375A GLU* 1.3 81.8 - - + +
377A TYR* 1.4 62.4 + - - +
379A MET* 3.2 10.6 + - + +
380A TRP* 2.9 30.1 + - - +
418A TYR* 4.8 5.6 - - + +
435A ARG* 3.9 35.0 - - + +
438A LEU* 3.7 25.3 - - + +
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A HIS* 3.7 24.9 - - - -
172A ASP* 4.2 7.7 + - - -
173A LEU* 3.6 34.6 + - + +
219A LEU* 3.9 16.5 - - + +
220A GLU* 3.4 61.4 + - + -
223A SER* 3.8 14.8 + - - +
224A LEU* 4.1 10.4 - - + +
374A ASP* 3.7 30.3 - - - +
375A GLU 3.2 0.6 - - - -
376A THR* 1.4 80.3 + - - +
378A TYR* 1.3 59.2 + - - +
380A TRP* 3.7 4.4 - - - +
381A ALA* 2.8 33.4 + - - +
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Residues in contact with TYR 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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219A LEU* 3.8 9.0 - - - +
358A MET* 3.5 47.5 + - + +
361A VAL* 3.9 22.9 - - + +
362A LYS* 3.9 24.0 + - + +
365A LEU* 4.1 15.5 - - + -
375A GLU* 3.3 11.8 + - - +
377A TYR* 1.3 76.5 - - - +
379A MET* 1.3 66.5 + - + +
382A LEU* 2.9 46.6 + - + +
401A GLU* 5.1 3.1 + - - -
402A THR* 3.7 16.1 - - + +
407A THR* 4.6 8.5 + - - +
410A PHE* 3.7 32.8 - + - -
411A ILE* 4.3 2.5 - - + -
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Residues in contact with MET 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 3.4 18.2 - - + +
376A THR* 3.2 12.2 + - + +
378A TYR* 1.3 76.8 - - + +
380A TRP* 1.3 65.9 + - - +
382A LEU* 3.6 1.1 + - - -
383A ALA* 3.2 20.6 + - - +
410A PHE* 4.6 7.4 - - + -
411A ILE* 3.5 28.9 - - + -
414A ASN* 3.5 44.0 - - + +
418A TYR* 4.2 12.1 - - + +
438A LEU* 3.8 25.1 - - + +
439A ALA* 4.0 21.1 - - + +
442A ALA* 3.6 14.4 - - + +
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Residues in contact with TRP 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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173A LEU* 3.8 39.6 - - + +
223A SER* 3.8 32.1 - - - -
226A PHE* 3.7 29.4 - - + -
227A ARG* 4.2 13.2 - - - -
229A GLN 5.4 1.8 - - - -
376A THR 2.9 17.6 + - - +
377A TYR 3.7 4.3 - - - +
379A MET* 1.3 75.9 - - - +
381A ALA* 1.3 62.3 + - - +
383A ALA* 3.3 6.9 + - - +
384A PHE* 3.0 63.8 + + + +
385A PHE* 4.7 3.6 - + - -
438A LEU* 4.0 23.1 - - + +
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Residues in contact with ALA 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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219A LEU* 3.7 27.1 - - + -
223A SER* 3.9 7.0 - - - +
354A TYR* 4.2 0.8 - - - -
358A MET* 4.1 9.6 - - - -
377A TYR 2.8 18.6 + - - +
378A TYR 3.9 2.7 - - - +
380A TRP* 1.3 82.3 - - - +
382A LEU* 1.3 66.9 + - - +
385A PHE* 2.9 44.0 + - + +
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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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354A TYR* 3.6 12.3 - - - +
358A MET* 3.8 4.3 - - + +
378A TYR* 2.9 24.2 + - + +
379A MET* 3.8 4.3 - - - +
381A ALA* 1.3 74.4 - - - +
383A ALA* 1.3 66.4 + - - +
386A MET* 3.0 52.4 + - - +
402A THR* 4.0 13.9 - - + -
407A THR* 3.8 28.9 - - + -
411A ILE* 4.0 21.8 - - + -
442A ALA* 3.6 29.4 - - + +
445A GLU* 4.6 2.9 - - + -
446A LEU* 4.1 5.4 - - + -
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Residues in contact with ALA 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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379A MET 3.2 15.2 + - - +
380A TRP* 3.8 4.7 - - - +
382A LEU* 1.3 78.8 - - - +
384A PHE* 1.3 63.5 + - - +
387A ALA* 3.2 25.1 + - - +
441A LYS* 4.0 27.4 - - + +
442A ALA* 4.1 5.4 - - - +
445A GLU* 3.8 15.3 - - + +
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Residues in contact with PHE 384 (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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226A PHE* 3.6 37.2 - + + -
229A GLN* 3.5 28.0 - - + -
231A PRO* 3.5 42.5 - - + +
234A LEU* 4.1 9.9 - - + -
346A CYS* 4.5 7.4 - - - -
380A TRP* 3.0 47.1 + + + +
381A ALA 4.0 1.3 - - - +
382A LEU 3.3 0.2 - - - -
383A ALA* 1.3 77.6 - - - +
385A PHE* 1.3 85.8 + + + +
387A ALA 3.3 1.6 + - - -
388A PHE* 3.0 24.7 + - + +
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Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 5.3 0.4 - - + -
222A VAL* 3.8 27.8 - - + -
223A SER* 5.1 1.8 - - - -
226A PHE* 4.0 17.7 - + + -
346A CYS* 3.6 32.5 - - + -
349A PHE* 3.7 33.4 - + - -
350A LEU* 3.9 13.8 - - + +
354A TYR* 3.6 18.8 - + + -
380A TRP* 4.7 6.1 - + - -
381A ALA* 2.9 46.1 + - + +
384A PHE* 1.3 86.8 - + - +
386A MET* 1.4 61.1 + - - +
388A PHE* 3.4 2.9 + - - +
389A ASN* 2.9 29.1 + - - +
399A VAL* 4.8 0.2 - - - -
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Residues in contact with MET 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.7 10.8 - - - +
382A LEU* 3.0 38.9 + - - +
385A PHE* 1.4 75.9 - - - +
387A ALA* 1.3 61.3 + - - +
389A ASN* 3.4 2.8 + - - +
390A ARG* 3.1 24.9 + - - +
399A VAL* 4.0 33.3 - - + +
402A THR* 3.2 33.7 - - - +
403A LEU* 4.0 21.5 - - + -
445A GLU* 3.6 16.6 - - + +
446A LEU* 3.9 8.5 - - + -
449A THR* 4.1 16.2 + - + +
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Residues in contact with ALA 387 (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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231A PRO* 3.6 20.6 - - + -
232A GLU* 4.0 13.4 - - - +
383A ALA 3.2 23.0 + - - +
384A PHE 3.5 3.6 - - - +
386A MET* 1.3 75.5 - - - +
388A PHE* 1.3 57.5 + - - +
390A ARG* 3.5 6.7 + - - +
391A ALA* 2.9 30.8 + - - +
445A GLU* 3.6 19.7 + - - +
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Residues in contact with PHE 388 (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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231A PRO* 3.4 29.1 - - + +
234A LEU* 3.7 19.3 - - + -
235A ALA* 3.5 29.2 - - + -
343A ARG* 4.2 12.3 - - + -
346A CYS* 3.5 30.3 - - + -
347A SER* 4.1 13.0 - - - -
350A LEU* 3.6 16.2 - - + -
384A PHE* 3.0 17.2 + + + +
385A PHE* 3.7 5.4 - - - +
386A MET 3.3 0.2 - - - -
387A ALA* 1.3 74.5 - - - +
389A ASN* 1.3 65.5 + - - +
391A ALA* 3.1 1.9 + - - +
392A ALA* 2.9 32.1 + - + +
394A PHE* 3.8 24.7 - + - -
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Residues in contact with ASN 389 (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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350A LEU* 3.8 10.9 - - + +
385A PHE 2.9 18.8 + - - +
386A MET* 3.4 5.3 + - - +
388A PHE* 1.3 77.3 - - - +
390A ARG* 1.3 59.7 + - - +
392A ALA 3.6 0.3 + - - -
393A SER* 3.2 2.6 + - - -
394A PHE* 2.9 62.5 + - - +
395A ARG 3.2 23.2 + - - -
396A PRO* 4.4 1.8 - - - +
398A LEU* 3.7 14.7 - - - +
399A VAL* 3.9 31.0 - - + +
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Residues in contact with ARG 390 (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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232A GLU* 4.6 12.6 + - - -
386A MET 3.1 11.6 + - - +
387A ALA* 3.7 4.8 - - - +
389A ASN* 1.3 78.8 - - - +
391A ALA* 1.3 64.5 + - - +
393A SER* 3.1 16.1 + - - +
394A PHE 5.7 0.4 - - - -
445A GLU* 2.9 40.4 + - - -
448A ALA* 3.7 19.3 - - - +
449A THR* 3.6 28.3 + - + +
452A GLU* 2.9 43.1 + - - +
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Residues in contact with ALA 391 (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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232A GLU* 4.0 26.9 - - + -
235A ALA* 3.9 17.5 - - + -
237A VAL* 3.8 24.8 - - + +
387A ALA 2.9 18.3 + - - +
388A PHE 3.1 3.8 + - - +
390A ARG* 1.3 77.9 - - - +
392A ALA* 1.3 59.1 + - - +
393A SER* 3.4 4.2 + - - -
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Residues in contact with ALA 392 (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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235A ALA* 4.0 13.7 - - + +
388A PHE* 2.9 31.7 + - + +
389A ASN 4.1 1.6 - - - +
391A ALA* 1.3 76.4 - - - +
393A SER* 1.3 70.7 + - - +
394A PHE* 3.2 31.9 + - + -
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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