Contacts of the helix formed by residues 394 - 407 (chain D) in PDB entry 2QMR
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 LEU 394 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297D LEU* 4.4 17.0 - - + -
301D ILE* 3.8 31.0 - - + -
383D LEU* 4.2 11.4 - - + -
386D LEU* 4.8 4.5 - - + +
387D ALA* 3.6 35.9 - - + +
390D TYR* 4.0 16.9 - - + +
391D ARG 3.1 13.7 + - - +
392D ASP 3.0 1.0 - - - -
393D GLU* 1.3 77.4 - - - +
395D LEU* 1.3 64.5 + - - +
396D PRO 3.4 0.4 - - - -
397D HIS* 3.0 17.8 + - + +
398D ILE* 3.2 15.8 + - + +
424D ILE* 4.1 12.6 - - + -
428D CYS* 4.0 8.1 - - - -
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Residues in contact with LEU 395 (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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392D ASP* 3.0 17.3 + - + +
394D LEU* 1.3 77.2 - - - +
396D PRO* 1.4 63.5 - - + +
398D ILE* 2.8 37.8 + - + -
399D LEU* 2.9 34.9 + - + +
424D ILE* 4.2 1.3 - - + -
428D CYS* 3.6 31.4 - - + +
431D GLY* 3.4 44.0 - - - +
432D MET* 3.9 18.4 - - - +
435D TYR* 5.0 0.2 - - + -
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Residues in contact with PRO 396 (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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396C PRO* 4.9 4.7 - - - +
392D ASP 3.6 6.7 - - - +
393D GLU* 3.4 17.9 - - - +
395D LEU* 1.4 92.5 - - + +
397D HIS* 1.3 69.5 + - + +
399D LEU* 5.7 0.7 - - + -
400D PRO* 3.6 19.6 - - + +
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Residues in contact with HIS 397 (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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294D VAL* 4.7 5.4 + - - +
297D LEU* 3.9 27.4 - - + +
298D PRO* 3.5 41.4 - - + +
301D ILE* 3.2 35.0 - - + +
302D PRO* 5.3 1.3 - - + +
393D GLU 3.9 19.0 + - - -
394D LEU* 3.0 9.3 + - + +
395D LEU 3.0 1.2 - - - -
396D PRO* 1.3 86.4 + - + +
398D ILE* 1.3 60.3 + - - +
400D PRO* 4.6 3.9 - - - +
401D LEU* 4.7 6.1 - - - +
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Residues in contact with ILE 398 (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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301D ILE* 3.6 26.2 - - + -
305D VAL* 3.9 18.6 - - + -
383D LEU* 4.0 20.0 - - + -
394D LEU* 3.2 12.0 + - + +
395D LEU* 2.8 41.1 + - + +
397D HIS* 1.3 80.2 - - - +
399D LEU* 1.3 59.9 + - + +
400D PRO* 3.5 1.6 - - - -
401D LEU* 3.0 12.1 + - + +
402D LEU* 2.8 32.2 + - + -
420D VAL* 3.9 20.0 - - + -
424D ILE* 3.9 18.6 - - + -
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Residues in contact with LEU 399 (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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395D LEU* 2.9 42.1 + - + +
396D PRO* 5.7 0.7 - - + -
398D ILE* 1.3 71.1 - - + +
400D PRO* 1.4 67.2 - - + +
402D LEU* 3.0 17.7 + - + +
403D LYS* 2.8 50.7 + - + +
432D MET* 3.8 29.8 - - + -
435D TYR* 3.6 39.5 - - + +
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Residues in contact with PRO 400 (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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393C GLU* 5.2 5.4 - - + +
396C PRO* 3.4 39.3 - - + -
397C HIS* 3.4 33.0 + - + +
395D LEU 4.0 0.4 - - - +
396D PRO* 3.6 23.8 - - + +
397D HIS 4.7 4.3 - - - +
398D ILE 3.6 2.0 - - - -
399D LEU* 1.4 93.6 - - + +
401D LEU* 1.3 60.2 + - + +
403D LYS* 3.8 4.9 - - + +
404D GLU* 3.6 14.0 + - - +
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Residues in contact with LEU 401 (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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396C PRO* 5.9 4.0 - - + +
301D ILE* 4.4 7.4 - - + -
302D PRO* 4.0 26.5 - - + +
305D VAL* 3.7 42.4 - - + -
397D HIS 4.7 5.2 - - - +
398D ILE* 3.0 13.1 + - + +
400D PRO* 1.3 78.4 - - + +
402D LEU* 1.3 65.8 - - - +
404D GLU* 3.2 17.4 + - - +
405D LEU* 3.2 31.5 + - + +
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Residues in contact with LEU 402 (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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398D ILE* 2.8 14.6 + - + +
399D LEU* 3.3 28.9 - - + +
401D LEU* 1.3 72.7 - - - +
403D LYS* 1.3 68.4 + - + +
405D LEU* 2.8 15.6 + - + +
406D LEU* 3.0 40.0 + - + +
417D GLY* 3.4 28.3 - - - +
420D VAL* 4.1 18.4 - - + +
421D LEU* 4.2 18.6 - - + +
424D ILE* 4.1 24.9 - - + -
432D MET* 4.4 3.1 - - + -
439D LEU* 5.5 0.9 - - + -
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Residues in contact with LYS 403 (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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294C VAL* 3.6 46.0 - - + +
295C ARG* 5.0 3.6 - - - +
298C PRO* 4.6 6.6 - - + +
397C HIS* 5.1 4.0 - - + +
399D LEU* 2.8 38.9 + - + +
400D PRO* 3.8 9.6 - - + +
402D LEU* 1.3 74.5 - - + +
404D GLU* 1.3 63.2 + - - +
406D LEU* 4.0 2.7 + - + +
407D PHE* 3.2 38.3 - - + +
435D TYR* 4.0 34.6 - - - +
438D GLU* 4.6 7.9 + - - -
439D LEU* 4.8 15.2 - - - +
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Residues in contact with GLU 404 (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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298C PRO* 3.2 46.3 - - + +
299C LYS* 5.8 2.6 - - - +
397C HIS* 5.8 0.2 - - - +
400D PRO 3.6 7.8 + - - +
401D LEU* 3.2 21.3 + - - +
402D LEU 3.1 0.8 - - - -
403D LYS* 1.3 80.1 - - - +
405D LEU* 1.3 71.3 + - + +
407D PHE 4.2 1.2 - - - -
408D HIS* 3.6 34.5 + - + +
413D VAL* 5.8 0.2 - - + -
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Residues in contact with LEU 405 (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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305D VAL* 3.6 31.9 - - + -
309D LYS* 5.4 4.7 - - - -
401D LEU* 3.2 23.6 - - + +
402D LEU* 2.8 12.7 + - + +
404D GLU* 1.3 82.9 - - + +
406D LEU* 1.3 63.2 + - - +
407D PHE 3.2 1.0 + - - -
408D HIS* 3.3 15.4 + - - +
413D VAL* 3.5 27.1 - - + +
414D LYS* 3.4 15.7 - - - -
416D SER* 4.1 9.6 - - - +
417D GLY* 3.6 28.7 - - - +
420D VAL* 4.4 4.7 - - + -
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Residues in contact with LEU 406 (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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402D LEU* 3.0 40.6 + - + +
403D LYS* 5.1 2.9 - - - +
404D GLU 3.5 0.2 - - - -
405D LEU* 1.3 77.5 - - - +
407D PHE* 1.3 76.1 + - + +
408D HIS 3.4 0.2 - - - -
414D LYS* 3.4 26.4 - - - +
417D GLY 3.6 29.2 - - - +
418D ILE* 3.8 19.5 - - + +
421D LEU* 4.1 15.9 - - + -
439D LEU* 3.7 30.7 - - + -
442D HIS* 3.5 18.5 + - + +
443D LEU* 5.4 1.8 - - + -
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Residues in contact with PHE 407 (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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294C VAL* 5.8 1.3 - - + -
295C ARG* 3.6 62.8 - - + +
299C LYS* 3.6 20.3 + - - +
403D LYS* 3.2 41.1 - - + +
404D GLU 4.0 4.3 + - - -
405D LEU 3.2 0.6 - - - -
406D LEU* 1.3 87.1 - - + +
408D HIS* 1.3 62.7 + - - +
409D HIS* 3.8 1.0 + - - -
414D LYS* 5.3 0.9 - - - -
438D GLU* 5.5 5.8 - - - -
439D LEU* 4.3 17.3 - - + -
442D HIS* 3.7 43.5 - + + -
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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