Contacts of the helix formed by residues 393 - 404 (chain D) in PDB entry 2B4J
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 HIS 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349D ASP* 2.8 53.7 + - + -
352D LEU* 3.6 19.1 - - + +
353D GLN* 4.0 14.4 - - + -
389D GLN 3.0 24.7 - - - +
390D ALA* 3.0 13.1 + - - +
392D LYS* 1.3 87.1 + - + +
394D THR* 1.3 62.9 + - - +
396D MET* 3.2 17.9 + - + +
397D ILE* 3.2 21.7 + - - +
443D GOL 2.5 44.2 + - - +
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Residues in contact with THR 394 (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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390D ALA 4.5 2.5 - - - +
391D GLN* 3.1 37.2 + - - +
392D LYS 3.6 2.0 + - - -
393D HIS* 1.3 74.6 - - - +
395D GLU* 1.3 78.6 + - - +
397D ILE* 3.0 14.3 + - + +
398D THR* 2.9 27.1 + - - -
443D GOL 3.8 0.2 + - - -
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Residues in contact with GLU 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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356D HIS* 3.5 14.1 - - + -
392D LYS 4.3 4.3 - - - +
394D THR* 1.3 87.4 + - - +
396D MET* 1.3 56.7 + - - +
398D THR* 3.2 11.3 + - - +
399D THR* 2.9 30.1 + - - -
443D GOL 2.6 39.6 + - - +
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Residues in contact with MET 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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352D LEU* 3.8 43.7 - - + +
355D ILE* 4.4 6.1 - - - -
356D HIS* 3.5 30.6 - - + -
359D ILE* 5.2 3.8 - - + +
380D LEU* 4.2 31.0 - - + -
385D VAL* 6.1 0.4 - - + -
390D ALA* 6.0 2.2 - - - -
393D HIS* 3.4 21.8 - - + +
394D THR 3.2 0.2 - - - -
395D GLU* 1.3 74.6 - - - +
397D ILE* 1.3 71.5 + - + +
399D THR* 3.2 4.2 + - - -
400D LEU* 3.1 27.1 + - + +
423D PHE* 4.7 11.2 - - + -
443D GOL 2.9 16.6 + - - +
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Residues in contact with ILE 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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390D ALA* 3.4 38.1 - - + +
391D GLN* 5.6 0.2 - - - -
393D HIS 3.3 9.0 - - - +
394D THR* 3.0 16.8 + - + +
396D MET* 1.3 83.1 - - + +
398D THR* 1.3 59.6 - - - +
400D LEU* 3.1 10.8 + - + +
401D LYS 2.9 23.9 + - - -
420D TYR* 3.7 28.0 - - + +
423D PHE* 4.5 30.3 - - + +
424D LYS* 5.6 3.1 - - + +
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Residues in contact with THR 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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394D THR* 2.9 15.1 + - - -
395D GLU* 3.3 13.4 - - - +
397D ILE* 1.3 73.1 - - - +
399D THR* 1.3 65.0 + - - +
401D LYS* 3.4 11.8 + - + +
402D LYS* 3.0 27.1 + - + +
420D TYR* 5.8 0.2 - - - -
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Residues in contact with THR 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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356D HIS* 2.5 36.9 + - + +
359D ILE* 3.8 31.0 - - + -
360D LYS* 4.5 10.8 - - + +
363D LEU* 5.9 0.2 - - + -
395D GLU 2.9 9.4 + - - -
396D MET 3.5 5.4 - - - -
397D ILE 3.2 0.2 - - - -
398D THR* 1.3 79.2 - - - +
400D LEU* 1.3 61.5 + - - +
402D LYS* 3.3 11.4 + - + +
403D ILE* 3.1 28.3 + - + +
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Residues in contact with LEU 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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359D ILE* 4.3 12.6 - - + -
377D LEU* 3.6 31.0 - - + -
380D LEU* 3.8 23.8 - - + -
396D MET* 3.1 22.0 + - + +
397D ILE* 3.1 14.2 + - - +
399D THR* 1.3 73.8 - - - +
401D LYS* 1.3 63.1 + - - +
403D ILE* 3.2 18.1 + - + +
404D ARG* 3.3 16.3 + - - +
416D SER* 3.7 12.0 - - - +
419D LEU* 4.0 11.2 - - + -
420D TYR* 4.1 15.0 - - + +
423D PHE* 3.9 24.0 - - + -
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Residues in contact with LYS 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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397D ILE 2.9 8.2 + - - +
398D THR* 3.4 15.3 - - + +
400D LEU* 1.3 75.2 - - - +
402D LYS* 1.3 62.2 + - - +
404D ARG* 2.7 39.8 + - - +
405D ARG* 3.2 32.8 + - - +
420D TYR* 3.6 39.4 + - + +
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Residues in contact with LYS 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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131A TRP* 4.4 28.6 - - + -
132A TRP* 5.2 2.4 - - - +
168B GLN* 3.6 32.5 + - - +
398D THR* 3.0 17.3 + - + +
399D THR* 3.3 13.2 + - + +
401D LYS* 1.3 77.5 - - - +
403D ILE* 1.3 66.1 + - + +
404D ARG 3.4 1.0 + - - -
405D ARG* 3.5 25.2 + - - +
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Residues in contact with ILE 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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131A TRP* 5.0 8.5 - - + -
359D ILE* 3.9 24.7 - - + -
363D LEU* 3.6 22.9 - - + -
373D CYS* 4.3 4.5 - - - -
377D LEU* 4.5 8.5 - - + -
399D THR* 3.1 21.9 + - + +
400D LEU* 3.2 9.1 + - + +
402D LYS* 1.3 81.9 - - + +
404D ARG* 1.3 65.7 + - - +
405D ARG 3.0 2.5 - - - -
406D PHE* 3.0 29.8 + - + +
412D ILE* 3.8 18.2 - - + +
413D MET* 3.9 5.7 - - - -
416D SER* 3.4 27.8 + - - -
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Residues in contact with ARG 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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400D LEU 3.3 8.8 + - - +
401D LYS* 2.7 43.6 - - - +
402D LYS 3.3 1.2 - - - -
403D ILE* 1.3 77.2 - - - +
405D ARG* 1.3 98.2 + - - +
406D PHE 3.4 0.2 - - - -
413D MET* 3.1 30.5 - - - +
416D SER* 3.3 9.9 - - - +
417D THR* 3.4 42.5 + - - +
420D TYR* 3.7 32.0 - - - -
421D ASN* 5.1 4.4 + - - -
424D LYS* 5.3 3.0 - - - +
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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