Contacts of the helix formed by residues 415 - 434 (chain B) in PDB entry 4MQP
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 THR 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ARG* 5.5 0.2 - - - +
413B ILE 4.3 6.1 - - - +
414B CYS* 1.3 74.7 - - - +
416B PRO* 1.4 75.9 - - - +
417B ALA* 3.6 8.7 + - - +
418B GLU* 3.0 36.1 + - - +
419B ILE* 3.0 21.2 + - - +
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Residues in contact with PRO 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 4.8 13.2 - - - +
347B GLU* 5.8 1.1 - - - +
414B CYS 4.4 1.8 - - - +
415B THR* 1.4 86.1 - - + +
417B ALA* 1.3 63.9 + - - +
419B ILE* 3.2 8.9 + - + +
420B THR* 3.0 26.6 + - - -
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 3.3 9.2 + - - +
416B PRO* 1.3 79.0 - - - +
418B GLU* 1.3 57.4 + - + +
420B THR* 3.3 10.2 - - - +
421B GLN* 3.0 27.5 + - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 4.4 4.6 - - - +
45B TRP* 3.0 34.0 + - + -
58B LEU* 3.7 25.4 - - + +
413B ILE 4.1 2.1 - - - +
414B CYS* 3.3 15.8 - - + +
415B THR* 3.0 42.0 + - - +
417B ALA* 1.3 75.1 - - + +
419B ILE* 1.3 61.6 + - - +
421B GLN* 3.3 5.7 + - - +
422B ILE* 2.9 34.9 + - - +
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.6 30.7 - - + +
351B GLY* 3.6 35.9 - - - +
352B LEU* 3.7 17.0 - - + +
410B PRO* 3.7 26.2 - - + -
414B CYS* 3.6 22.9 - - + +
415B THR 3.0 16.5 + - - +
416B PRO* 3.2 9.4 + - + +
418B GLU* 1.3 73.2 - - - +
420B THR* 1.3 54.4 + - - +
422B ILE* 3.0 8.9 + - + +
423B THR* 2.8 33.1 + - + -
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Residues in contact with THR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLY 5.9 0.7 - - - -
355B GLY* 5.9 0.7 - - - -
416B PRO 3.0 14.2 + - - -
417B ALA* 3.3 13.7 - - - +
419B ILE* 1.3 75.4 - - - +
421B GLN* 1.3 58.1 + - - +
423B THR* 2.9 10.5 + - - +
424B SER* 2.9 31.8 + - - -
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.0 16.8 - - - -
58B LEU* 3.6 18.7 - - + +
395B ARG* 3.3 25.3 + - - +
396B GLY* 3.4 21.2 + - - -
397B VAL* 3.7 2.2 - - + +
417B ALA 3.0 11.8 + - - +
418B GLU* 3.6 9.9 - - - +
419B ILE 3.2 0.2 - - - -
420B THR* 1.3 81.0 - - - +
422B ILE* 1.3 62.7 + - - +
424B SER* 3.5 5.7 + - - -
425B ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.0 23.6 - - + -
59B ASP 5.3 0.4 - - - -
60B ALA* 3.9 30.5 - - + +
352B LEU* 5.1 2.0 - - + -
397B VAL* 4.1 9.2 - - + -
399B LEU* 4.9 0.3 - - - +
408B ALA* 3.8 28.5 - - + -
410B PRO* 4.2 20.6 - - + -
414B CYS* 4.3 14.8 - - - -
418B GLU 2.9 18.3 + - - +
419B ILE* 3.0 11.9 + - + +
421B GLN* 1.3 76.3 - - - +
423B THR* 1.3 65.7 + - + +
425B ALA* 3.3 4.9 + - - +
426B MET* 3.1 28.4 + - + +
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Residues in contact with THR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLY 4.1 2.2 + - - +
352B LEU* 3.9 35.2 - - + +
355B GLY* 3.3 29.9 - - - -
356B LEU* 3.8 26.7 - - + -
419B ILE* 2.8 20.8 + - + +
420B THR* 2.9 19.9 + - - +
422B ILE* 1.3 72.4 - - - +
424B SER* 1.3 55.0 + - - +
426B MET* 3.3 5.2 + - - +
427B VAL* 2.9 35.4 + - - +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLY 5.6 0.2 - - - -
395B ARG* 5.0 2.2 - - - -
420B THR* 2.9 21.7 + - - -
421B GLN* 3.7 7.6 - - - -
423B THR* 1.3 77.1 + - - +
425B ALA* 1.3 57.1 + - - +
427B VAL* 3.3 7.5 + - - +
428B GLU* 2.9 40.6 + - - +
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA* 4.6 5.2 - - - +
395B ARG* 3.9 28.0 - - + +
397B VAL* 3.7 26.0 - - + -
399B LEU* 4.1 9.4 - - + -
421B GLN 3.2 11.6 + - - +
422B ILE 3.3 8.3 + - - +
424B SER* 1.3 76.2 - - - +
426B MET* 1.3 58.0 + - - +
428B GLU* 3.3 2.3 + - - +
429B VAL* 2.9 33.3 + - - +
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LEU* 5.4 0.9 - - - -
356B LEU* 3.8 28.5 - - + -
375B GLY 3.6 20.0 - - - +
377B ILE* 3.7 11.9 - - + +
399B LEU* 3.6 25.8 - - + -
406B VAL* 3.6 33.1 - - + +
407B TYR* 3.8 5.8 - - - -
408B ALA* 3.7 22.0 - - - -
422B ILE* 3.1 21.5 + - - +
423B THR* 3.5 9.9 - - - +
425B ALA* 1.3 72.7 - - - +
427B VAL* 1.3 61.3 + - - +
429B VAL* 3.2 3.3 + - - +
430B ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLY 3.7 18.8 - - - +
356B LEU* 4.4 7.9 - - + -
358B THR* 3.8 22.4 - - - +
359B ALA* 4.2 16.2 - - + +
362B LEU* 3.6 14.1 - - + +
377B ILE* 4.2 4.9 - - - -
423B THR 2.9 22.3 + - - +
424B SER* 3.7 7.2 - - - +
426B MET* 1.3 74.4 - - - +
428B GLU* 1.3 61.8 + - - +
430B ALA* 3.2 4.9 + - - +
431B ARG* 2.9 47.7 + - - +
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Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ARG* 3.3 46.7 + - - +
424B SER* 2.9 26.6 + - - +
425B ALA 3.9 0.2 - - - +
427B VAL* 1.3 77.5 - - - +
429B VAL* 1.3 65.4 + - - +
431B ARG* 2.7 49.1 + - - +
432B LEU* 3.0 30.3 + - - +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B VAL* 4.4 5.2 - - + -
387B VAL* 5.9 0.2 - - - +
388B ALA* 3.7 42.4 - - + +
391B ALA* 4.4 5.8 - - + -
392B ALA* 4.2 11.4 - - + +
399B LEU* 4.2 15.5 - - + -
401B PRO* 4.6 0.4 - - + -
406B VAL* 3.6 28.9 - - + -
425B ALA 2.9 19.5 + - - +
426B MET 3.5 7.9 - - - +
428B GLU* 1.3 75.9 - - - +
430B ALA* 1.3 62.4 + - - +
432B LEU* 3.2 10.0 + - - +
433B VAL* 3.1 22.5 + - + +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.8 16.8 - - + +
364B ALA* 4.3 7.1 - - - +
365B VAL* 3.9 18.8 - - + +
377B ILE* 4.0 18.8 - - + -
379B CYS* 4.5 6.0 - - - -
406B VAL* 4.9 2.0 - - + +
426B MET 2.9 12.7 + - - +
427B VAL 3.2 7.6 + - - +
429B VAL* 1.3 77.9 - - - +
431B ARG* 1.3 61.7 + - - +
433B VAL* 3.5 11.9 + - - +
434B GLY* 3.4 16.1 + - - -
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B THR* 5.7 1.2 + - - -
362B LEU* 3.6 31.9 - - + +
363B PRO* 6.1 1.7 - - - +
427B VAL* 2.9 26.1 + - - +
428B GLU* 2.7 47.7 + - - +
430B ALA* 1.3 78.0 - - - +
432B LEU* 1.3 63.6 + - + +
434B GLY* 3.3 17.7 + - - -
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B VAL* 4.1 25.8 - - + +
391B ALA* 3.4 33.2 - - + -
395B ARG* 4.7 11.9 - - - +
428B GLU* 3.0 20.0 + - + +
429B VAL* 3.2 5.6 + - - +
431B ARG* 1.3 76.1 - - + +
433B VAL* 1.3 66.1 + - - +
434B GLY 3.2 4.9 + - - -
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ALA* 4.1 9.0 - - + -
379B CYS* 4.4 13.5 - - + -
381B ARG* 3.0 54.7 + - + +
382B PRO 5.0 1.6 - - - +
383B VAL* 3.9 36.8 - - + -
384B ASP 5.4 0.9 - - - +
387B VAL* 5.3 4.7 - - + +
429B VAL* 3.1 19.6 + - + +
430B ALA* 3.6 11.7 - - - +
431B ARG 3.4 0.2 - - - -
432B LEU* 1.3 76.4 - - - +
434B GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B PRO* 4.7 15.2 - - - +
364B ALA* 3.5 23.1 - - - +
381B ARG* 4.0 12.2 + - - -
430B ALA 3.4 5.0 + - - -
431B ARG 3.3 17.3 + - - -
432B LEU 3.1 5.5 - - - -
433B VAL* 1.3 83.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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