Contacts of the helix formed by residues 362 - 382 (chain D) in PDB entry 2QJK
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 MET 362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361D PRO* 1.3 75.4 - - + +
363D PHE* 1.3 66.1 + - - +
365D ILE* 2.9 21.6 + - - +
366D TYR* 3.5 35.4 + - + +
411D LEU* 3.7 23.8 - - + -
414D ILE* 4.2 21.1 - - + -
415D GLU* 2.5 30.6 + - + +
416D LYS 5.8 0.9 - - - +
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Residues in contact with PHE 363 (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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116D LEU 3.6 19.7 - - - -
117D TYR* 4.3 16.4 - + - -
121D TYR* 4.5 1.8 - - - -
350D ASP* 4.1 3.4 - - - -
357D GLY* 4.4 14.1 - - - -
360D ARG* 3.2 56.5 - - + +
362D MET* 1.3 75.3 - - - +
364D LYS* 1.3 70.7 + - - +
365D ILE 2.7 2.6 + - - -
366D TYR* 2.9 15.4 + - - +
367D PHE* 3.0 33.4 + + + -
403D TYR* 3.4 17.4 - + - -
408D LEU* 3.5 27.4 - - + -
411D LEU* 4.0 13.0 - - + +
415D GLU* 2.9 9.9 + - - +
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Residues in contact with LYS 364 (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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117D TYR* 4.5 12.4 + - + +
357D GLY 3.6 9.9 - - - +
358D ARG* 2.8 42.9 + - - +
359D TYR* 4.8 0.2 - - - +
360D ARG 2.9 26.6 + - - +
361D PRO* 3.8 16.8 - - + +
363D PHE* 1.3 81.8 - - + +
365D ILE* 1.3 64.2 + - + +
367D PHE* 4.3 2.7 - - - -
368D TRP* 2.9 42.6 + - + +
418D VAL* 6.5 0.2 - - - -
503D LOP 5.2 2.4 + - - -
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Residues in contact with ILE 365 (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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361D PRO 4.1 10.8 - - - +
362D MET* 2.9 13.6 + - - +
363D PHE 2.7 4.2 + - - -
364D LYS* 1.3 77.5 - - + +
366D TYR* 1.3 78.5 + - + +
368D TRP* 3.5 5.3 + - + +
369D LEU* 3.1 36.5 + - + +
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Residues in contact with TYR 366 (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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362D MET* 3.6 34.1 - - + +
363D PHE 2.9 7.0 + - - +
365D ILE* 1.3 81.7 - - + +
367D PHE* 1.3 60.3 + - - +
369D LEU* 3.1 11.8 + - + -
370D LEU* 2.8 21.8 + - - +
399D TYR* 2.7 33.0 + + - +
403D TYR* 3.9 11.6 - - + -
407D ILE* 3.2 43.7 - - + -
411D LEU* 3.6 26.9 - - + -
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Residues in contact with PHE 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 3.8 26.9 - + - -
116D LEU* 4.0 8.7 - - + -
117D TYR* 3.3 55.2 - + + -
363D PHE* 3.0 40.9 + + + +
364D LYS* 3.7 4.0 - - - +
366D TYR* 1.3 76.5 - - - +
368D TRP* 1.3 94.7 + + - +
370D LEU* 2.8 28.6 + - + +
371D ALA* 3.0 7.9 + - + +
403D TYR* 3.9 19.8 - + - -
503D LOP 4.3 10.5 - - + -
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Residues in contact with TRP 368 (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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117D TYR* 4.3 11.8 - + - -
364D LYS* 2.9 33.6 + - + +
365D ILE* 4.1 6.3 - - + +
367D PHE* 1.3 99.2 - + - +
369D LEU* 1.3 58.2 + - - +
371D ALA* 3.3 12.6 + - + +
372D ALA* 2.8 28.9 + - - +
503D LOP 3.8 68.0 - - + -
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Residues in contact with LEU 369 (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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365D ILE* 3.1 27.9 + - + +
366D TYR* 3.1 18.1 + - + +
367D PHE 3.1 0.4 - - - -
368D TRP* 1.3 73.4 - - - +
370D LEU* 1.3 55.8 + - - +
372D ALA* 3.2 9.0 + - + +
373D ASP* 2.6 36.7 + - - +
399D TYR* 3.2 36.1 - - + +
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Residues in contact with LEU 370 (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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113D PHE* 4.1 18.6 - - + -
116D LEU* 4.2 7.6 - - + -
366D TYR 2.8 11.7 + - - +
367D PHE* 2.8 18.5 + - + +
369D LEU* 1.3 76.8 - - - +
371D ALA* 1.3 60.7 + - - +
373D ASP* 3.0 5.1 + - + +
374D PHE* 2.9 22.5 + - - +
399D TYR* 3.6 12.3 - - + -
400D TRP* 3.5 36.1 - - + -
403D TYR* 3.3 51.6 - - + -
404D PHE* 3.9 13.0 - - + -
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Residues in contact with ALA 371 (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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113D PHE* 4.2 21.5 - - + -
367D PHE* 3.0 13.0 + - + +
368D TRP* 3.5 26.7 - - + +
370D LEU* 1.3 76.9 - - - +
372D ALA* 1.3 64.8 + - - +
373D ASP 3.0 0.7 + - - -
374D PHE* 3.0 12.7 + - - +
375D VAL* 3.0 18.3 + - + +
503D LOP 4.6 19.4 - - + +
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Residues in contact with ALA 372 (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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368D TRP 2.8 20.5 + - - +
369D LEU* 3.5 12.3 - - + +
371D ALA* 1.3 73.4 - - - +
373D ASP* 1.3 58.0 + - - +
375D VAL* 3.3 8.3 + - - +
376D ILE* 2.8 41.7 + - + +
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Residues in contact with ASP 373 (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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369D LEU 2.6 16.7 + - - +
370D LEU* 3.1 14.8 - - + +
372D ALA* 1.3 71.0 - - - +
374D PHE* 1.3 57.4 + - - +
376D ILE* 2.9 15.0 + - - +
377D LEU* 2.5 45.6 + - - +
396D ALA* 2.7 51.3 - - - +
399D TYR* 3.8 12.7 - - + +
400D TRP* 3.6 16.0 + - + +
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Residues in contact with PHE 374 (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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109D TYR* 3.7 44.9 - + - -
113D PHE* 3.7 26.0 - + + -
300D PRO* 4.0 24.9 - - + +
301D PHE* 4.7 9.4 - + - -
370D LEU 2.9 15.2 + - - +
371D ALA 3.4 8.1 - - - +
373D ASP* 1.3 71.2 - - - +
375D VAL* 1.3 61.2 + - - +
377D LEU* 3.4 11.0 - - + +
378D THR* 2.8 32.5 + - - -
400D TRP* 4.0 25.1 - + + -
503D LOP 3.6 42.8 - - + -
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Residues in contact with VAL 375 (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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371D ALA* 3.0 16.3 + - + +
372D ALA* 3.3 10.3 - - - +
374D PHE* 1.3 75.0 - - - +
376D ILE* 1.3 70.2 + - + +
378D THR* 3.0 9.2 + - - -
379D TRP* 2.8 24.2 + - + +
503D LOP 4.4 31.0 - - + -
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Residues in contact with ILE 376 (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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372D ALA* 2.8 41.0 + - + +
373D ASP* 3.3 14.8 - - - +
375D VAL* 1.3 74.7 - - + +
377D LEU* 1.3 63.8 + - - +
379D TRP* 3.0 19.3 + - + +
380D VAL* 2.8 26.1 + - + +
392D ILE* 4.0 27.1 - - + -
396D ALA* 5.0 6.7 - - + -
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Residues in contact with LEU 377 (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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300D PRO* 3.6 15.8 - - + +
303D ALA* 3.4 33.8 - - + +
304D ILE* 3.5 36.1 - - + +
373D ASP* 2.5 35.9 + - - +
374D PHE* 3.4 14.1 - - + +
376D ILE* 1.3 72.1 - - - +
378D THR* 1.3 62.8 + - - +
380D VAL* 2.7 24.2 - - + +
381D GLY* 3.2 4.5 + - - -
393D SER* 5.0 1.3 - - - +
396D ALA* 3.9 23.3 - - + +
397D SER* 4.4 3.4 - - - +
400D TRP* 4.3 12.8 - - + -
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Residues in contact with THR 378 (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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296D TRP* 4.0 19.1 - - + +
299D LEU* 3.6 32.9 - - + +
300D PRO* 3.4 23.5 - - + +
374D PHE* 2.8 23.7 + - - -
375D VAL* 3.3 9.7 - - - -
377D LEU* 1.3 76.5 - - - +
379D TRP* 1.3 67.0 + - - +
381D GLY* 2.9 13.0 + - - -
382D ALA 3.6 4.9 + - - -
503D LOP 4.5 9.6 - - + +
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Residues in contact with TRP 379 (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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375D VAL* 2.8 15.7 + - + +
376D ILE* 3.2 21.1 - - + +
378D THR* 1.3 79.2 - - - +
380D VAL* 1.3 92.1 + - + +
382D ALA* 3.3 10.5 - - + +
383D GLN* 3.2 34.4 + - + +
389D TYR* 3.6 24.7 - + - -
392D ILE* 4.3 16.2 - - + -
114E MET* 3.3 56.3 + - + +
115E GLY 3.7 13.4 + - - -
116E THR* 4.2 10.6 + - + -
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Residues in contact with VAL 380 (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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303D ALA* 4.1 10.5 - - + -
306D ARG* 3.1 10.7 + - - -
376D ILE* 2.8 13.5 + - + +
377D LEU* 2.7 29.2 - - - +
379D TRP* 1.3 96.0 - - + +
381D GLY* 1.3 54.3 + - - +
382D ALA 2.8 4.9 - - - -
383D GLN* 2.7 33.5 + - + +
389D TYR* 4.8 7.9 - - + +
392D ILE* 3.9 26.7 - - + -
393D SER* 4.6 18.4 - - - +
396D ALA* 5.6 0.4 - - + -
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Residues in contact with GLY 381 (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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293D VAL* 4.3 4.5 - - - +
299D LEU* 3.9 14.1 - - - +
302D TYR* 3.1 37.6 - - - -
303D ALA* 4.2 9.6 - - - -
306D ARG* 3.3 12.1 + - - -
377D LEU 3.2 7.5 + - - -
378D THR 2.9 9.6 + - - -
380D VAL* 1.3 78.2 - - - +
382D ALA* 1.3 56.2 - - - +
383D GLN 3.9 0.5 - - - +
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Residues in contact with ALA 382 (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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293D VAL* 4.5 17.7 - - + +
299D LEU* 4.2 16.1 - - + +
378D THR 3.6 1.8 + - - -
379D TRP* 3.3 15.5 + - + +
380D VAL 2.8 0.4 - - - -
381D GLY* 1.3 78.3 - - - +
383D GLN* 1.3 68.3 + - - +
115E GLY 4.8 6.1 - - - +
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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
------------------------------------------------------------
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