Contacts of the helix formed by residues 394 - 412 (chain D) in PDB entry 2XLR
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 ASP 394 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D PHE* 1.3 76.7 - - - +
395D ILE* 1.3 57.8 + - - +
396D PRO* 3.4 14.6 - - - +
397D ALA* 3.3 33.0 + - + +
398D THR* 2.5 32.4 + - - -
424D LEU* 4.6 17.5 + - + +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.5 18.8 - - + +
378D GLY* 3.7 31.6 - - - +
379D ASP* 5.9 1.1 - - - +
381D ILE* 4.3 4.3 - - + -
382D GLN* 3.7 34.5 - - + +
385D ILE* 4.4 4.0 - - + -
393D PHE* 3.0 42.2 + - + +
394D ASP* 1.3 68.7 - - - +
396D PRO* 1.3 69.8 - - + +
398D THR* 2.8 7.7 + - - -
399D ASN* 2.6 47.8 + - - +
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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
----------------------------------------------------------
382D GLN* 5.4 3.6 - - - +
394D ASP* 3.4 12.3 - - - +
395D ILE* 1.3 97.9 - - + +
397D ALA* 1.3 63.3 + - - +
399D ASN* 3.3 7.9 + - - +
400D LYS* 2.9 45.3 + - - +
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Residues in contact with ALA 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D ASP* 3.3 34.7 + - + +
395D ILE 3.1 0.6 - - - -
396D PRO* 1.3 80.4 - - - +
398D THR* 1.3 52.3 + - - +
400D LYS* 3.4 8.3 + - - +
401D THR* 2.4 36.7 + - - -
424D LEU* 4.1 17.6 - - + +
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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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82D GLU 4.7 0.4 - - - +
83D CYS* 3.7 36.7 - - + +
325D TYR* 3.7 20.6 - - + -
393D PHE* 4.2 11.5 - - + -
394D ASP 2.5 26.9 + - - -
395D ILE* 2.8 6.9 + - - -
397D ALA* 1.3 74.5 - - - +
399D ASN* 1.3 66.4 + - - -
401D THR* 3.0 8.7 + - - -
402D PHE* 2.9 25.0 + - + -
424D LEU* 3.9 18.7 - - + +
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Residues in contact with ASN 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 2.4 36.3 + - - -
374D TYR* 3.5 15.6 + - + +
375D THR* 3.8 32.7 + - - +
395D ILE* 2.6 32.3 + - - +
396D PRO* 3.5 11.3 - - - +
398D THR* 1.3 72.0 - - - +
400D LYS* 1.3 69.3 + - - +
402D PHE* 2.9 25.5 + - - +
403D LEU* 3.1 17.1 + - - +
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Residues in contact with LYS 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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371D GLU* 5.5 4.3 - - - +
396D PRO* 2.9 44.3 + - - +
397D ALA* 3.6 10.8 - - - +
398D THR 3.3 0.2 - - - -
399D ASN* 1.3 82.8 - - - +
401D THR* 1.3 65.3 + - - +
403D LEU* 3.2 35.9 - - + +
404D GLU* 3.2 14.3 + - - +
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Residues in contact with THR 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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80D PRO* 4.5 4.7 - - + +
82D GLU* 5.0 6.7 - - + -
83D CYS* 3.9 17.7 - - - -
397D ALA 2.4 25.6 + - - -
398D THR* 3.0 8.8 + - - -
400D LYS* 1.3 77.2 - - - +
402D PHE* 1.3 62.2 + - - +
404D GLU* 3.2 22.0 + - - +
405D TRP* 3.2 13.0 + - - +
421D TYR* 3.9 33.8 - - + -
422D ARG 5.1 4.7 - - - +
424D LEU* 4.0 10.5 - - - +
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Residues in contact with PHE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY* 5.5 3.1 - - - -
80D PRO* 4.6 7.4 - - + -
83D CYS* 3.5 38.4 - - + -
324D TRP* 3.5 28.5 - + + -
325D TYR* 4.0 33.9 - + - -
374D TYR* 4.4 21.3 - - + -
398D THR* 2.9 22.5 + - + -
399D ASN* 2.9 14.6 + - - +
401D THR* 1.3 74.7 - - - +
403D LEU* 1.3 67.7 + - + +
405D TRP* 3.0 37.9 + + + +
406D LYS* 2.9 22.9 + - + +
501D NAP 5.1 4.3 - - - -
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ALA* 5.4 2.0 - - + -
371D GLU* 4.0 49.1 - - + +
374D TYR* 6.0 3.1 - - + -
399D ASN 3.1 12.5 + - - +
400D LYS* 3.2 34.3 - - + +
402D PHE* 1.3 79.2 - - + +
404D GLU* 1.3 63.9 + - + +
406D LYS* 3.1 11.4 + - + +
407D HIS* 2.9 24.5 + - - +
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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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400D LYS* 3.2 10.4 + - - +
401D THR* 3.2 24.0 + - - +
403D LEU* 1.3 78.8 - - + +
405D TRP* 1.3 54.0 + - - +
407D HIS* 3.2 6.6 + - - +
408D HIS* 2.7 52.9 + - + +
420D SER 4.8 2.4 - - - +
421D TYR* 3.7 26.7 - - + +
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Residues in contact with TRP 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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78D ASP* 3.0 31.2 + - - -
79D GLY* 4.0 3.8 - - - -
80D PRO* 3.8 21.3 - - + -
102D TYR* 3.1 26.5 - + - -
212D TYR* 4.2 5.2 - + - -
324D TRP* 5.9 2.7 - + - -
401D THR 3.2 8.4 + - - +
402D PHE* 3.0 39.0 + + + +
404D GLU* 1.3 82.4 - - - +
406D LYS* 1.3 100.9 + - + +
408D HIS* 3.1 2.6 + - - +
409D LYS* 3.1 42.5 + - + +
416D PHE* 3.6 18.3 - + - -
421D TYR* 3.8 9.8 - - - +
501D NAP 3.6 28.9 - - - -
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Residues in contact with LYS 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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212D TYR* 3.4 23.0 + - - -
240D TYR* 4.8 7.6 + - - +
324D TRP* 4.9 13.5 - - + -
370D ALA* 4.7 20.2 - - + -
402D PHE* 2.9 18.3 + - + +
403D LEU* 3.6 14.4 - - + +
405D TRP* 1.3 110.0 - - + +
407D HIS* 1.3 62.5 + - - +
409D LYS* 3.1 36.3 + - + +
410D LYS* 3.2 18.2 + - - +
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Residues in contact with HIS 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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403D LEU 2.9 16.0 + - - +
404D GLU* 3.5 7.6 - - - +
406D LYS* 1.3 77.9 - - - +
408D HIS* 1.3 67.1 + - - +
409D LYS 3.2 0.3 + - - -
410D LYS* 3.2 14.7 + - + +
411D GLU* 2.7 55.8 + - + +
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Residues in contact with HIS 408 (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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404D GLU* 2.7 32.4 + - - +
405D TRP 3.1 6.0 + - - +
407D HIS* 1.3 77.9 - - - +
409D LYS* 1.3 60.7 + - - +
411D GLU* 3.5 20.4 + - - +
412D ASN 3.2 24.1 + - - +
415D THR* 5.3 0.5 + - - -
416D PHE* 3.8 17.7 - - + +
419D HIS* 3.0 44.6 + + + -
420D SER 5.2 2.7 - - - -
421D TYR* 2.6 40.6 + + - +
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Residues in contact with LYS 409 (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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78D ASP* 6.3 0.2 - - - +
212D TYR* 4.0 15.0 - - - -
215D GLU* 2.9 32.0 + - - -
240D TYR* 3.8 25.0 + - - +
405D TRP* 3.1 36.8 + - + +
406D LYS* 3.1 31.5 + - + +
408D HIS* 1.3 74.0 - - - +
410D LYS* 1.3 67.8 + - - +
412D ASN 3.4 0.6 - - - -
413D ILE* 3.3 40.5 + - + -
416D PHE* 3.7 37.9 - - + -
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Residues in contact with LYS 410 (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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238D MET 4.4 9.1 + - - -
239D GLY* 4.1 19.7 + - - -
240D TYR* 4.0 30.5 - - + -
241D LYS* 5.5 5.2 + - - +
406D LYS 3.2 12.2 + - - +
407D HIS* 3.4 17.5 - - + +
409D LYS* 1.3 79.8 - - - +
411D GLU* 1.3 65.6 + - + +
412D ASN* 4.4 0.2 - - - -
413D ILE 5.1 0.2 + - - -
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Residues in contact with GLU 411 (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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241D LYS* 5.5 6.2 - - - +
407D HIS* 2.7 48.5 + - + +
408D HIS* 3.8 21.9 - - - +
409D LYS 3.3 0.4 - - - -
410D LYS* 1.3 81.1 - - + +
412D ASN* 1.3 65.2 + - + +
419D HIS* 4.4 11.1 + - - -
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Residues in contact with ASN 412 (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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241D LYS* 4.8 6.5 - - - +
408D HIS 3.2 8.9 + - - +
409D LYS 3.4 2.9 - - - -
410D LYS 4.4 0.2 - - - -
411D GLU* 1.3 85.2 - - + +
413D ILE* 1.3 67.8 + - - +
414D MET* 3.3 14.2 + - - +
415D THR* 2.7 52.0 + - - +
416D PHE* 3.1 12.1 + - - +
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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