Contacts of the helix formed by residues 394 - 412 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C PHE* 1.3 75.0 - - - +
395C ILE* 1.3 53.3 + - - +
396C PRO* 3.3 13.8 - - - +
397C ALA* 3.2 34.2 + - + +
398C THR* 2.6 35.0 + - - -
424C LEU* 4.5 15.9 - - + +
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Residues in contact with ILE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.7 17.3 - - + +
378C GLY* 3.7 31.9 - - - +
379C ASP* 5.9 0.7 - - - +
381C ILE* 4.3 3.8 - - + -
382C GLN* 3.5 36.3 - - + +
385C ILE* 4.4 3.1 - - + -
393C PHE* 3.0 43.3 + - + +
394C ASP* 1.3 69.7 - - - +
396C PRO* 1.3 72.5 - - + +
398C THR* 2.9 7.9 + - - -
399C ASN* 2.7 41.1 + - - +
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Residues in contact with PRO 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLN* 5.6 2.0 - - - +
394C ASP* 3.3 11.7 - - - +
395C ILE* 1.3 98.2 - - + +
397C ALA* 1.3 61.3 + - - +
399C ASN* 3.4 7.5 + - - +
400C LYS* 2.9 45.2 + - - +
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ASP* 3.2 32.5 + - + +
395C ILE 3.2 0.8 - - - -
396C PRO* 1.3 78.4 - - - +
398C THR* 1.3 61.2 + - - +
400C LYS* 3.3 9.4 + - - +
401C THR* 2.9 26.8 + - - -
424C LEU* 3.9 20.7 - - + +
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Residues in contact with THR 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C CYS* 4.0 34.5 - - - +
325C TYR* 3.8 25.8 - - + -
328C ASN* 5.4 0.2 - - - +
393C PHE* 4.1 12.0 - - + -
394C ASP 2.6 22.9 + - - -
395C ILE* 2.9 7.2 + - - -
397C ALA* 1.3 74.7 - - - +
399C ASN* 1.3 65.6 + - - +
401C THR* 3.0 4.6 + - - -
402C PHE* 3.0 25.6 + - + -
424C LEU* 3.8 18.9 - - + +
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Residues in contact with ASN 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 2.3 35.9 + - - -
374C TYR* 3.6 19.2 + - + +
375C THR* 3.9 28.1 + - - +
378C GLY* 4.8 0.2 - - - -
395C ILE* 2.7 34.2 + - - +
396C PRO* 3.6 9.8 - - - +
398C THR* 1.3 73.3 - - - +
400C LYS* 1.3 73.8 + - - +
402C PHE* 3.1 19.4 + - - +
403C LEU* 3.1 17.0 + - + +
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Residues in contact with LYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C GLU* 5.5 5.4 - - - +
396C PRO* 2.9 49.1 + - - +
397C ALA* 3.6 10.8 - - - +
398C THR 3.2 0.2 - - - -
399C ASN* 1.3 87.6 - - - +
401C THR* 1.3 62.0 + - - +
403C LEU* 3.3 24.2 - - + +
404C GLU* 3.2 26.8 + - - +
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Residues in contact with THR 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 4.4 4.2 - - + +
82C GLU* 5.0 5.6 - - + -
83C CYS* 3.7 20.0 - - - -
397C ALA 2.9 15.2 + - - -
398C THR* 3.0 9.2 + - - -
400C LYS* 1.3 75.8 - - - +
402C PHE* 1.3 65.3 + - - +
404C GLU* 3.2 14.3 + - - +
405C TRP* 3.2 20.6 + - - +
421C TYR* 3.9 34.9 - - + -
422C ARG 5.0 2.2 + - - +
424C LEU* 4.2 13.8 - - - +
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Residues in contact with PHE 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLY* 5.6 2.7 - - - -
80C PRO* 4.9 5.4 - - + -
83C CYS* 3.6 30.3 - - + -
324C TRP 3.4 22.2 - - - -
325C TYR* 4.0 24.2 - + - -
374C TYR* 3.3 56.1 - + + -
398C THR* 3.0 32.5 + - + -
399C ASN* 3.1 11.2 + - - +
401C THR* 1.3 76.2 - - - +
403C LEU* 1.3 58.2 + - - +
405C TRP* 3.1 24.8 + + - +
406C LYS* 3.0 27.2 + - - +
501C NAP 5.0 3.4 - - - -
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Residues in contact with LEU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ALA* 5.4 1.1 - - + -
371C GLU* 4.1 47.3 - - + +
374C TYR* 4.7 12.1 - - + -
399C ASN* 3.1 12.9 + - + +
400C LYS* 3.3 34.3 - - + +
402C PHE* 1.3 75.4 - - - +
404C GLU* 1.3 64.6 + - + +
406C LYS* 3.4 10.3 + - + +
407C HIS* 3.1 23.4 + - - +
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Residues in contact with GLU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LYS* 3.2 15.8 + - - +
401C THR* 3.2 17.7 + - - +
403C LEU* 1.3 79.1 - - + +
405C TRP* 1.3 59.6 + - - +
407C HIS* 3.4 5.9 + - - +
408C HIS* 2.9 44.9 + - + +
420C SER 5.1 1.9 - - - +
421C TYR* 3.8 26.3 - - + -
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Residues in contact with TRP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 2.9 33.0 + - - -
79C GLY* 3.9 2.9 - - - -
80C PRO* 3.7 21.5 - - + -
102C TYR* 3.0 23.6 - - - -
212C TYR* 4.2 5.8 - + - -
374C TYR* 3.0 26.0 - - - -
401C THR 3.2 9.3 + - - +
402C PHE* 3.1 29.9 + + - +
404C GLU* 1.3 77.0 - - - +
406C LYS* 1.3 92.8 + - - +
408C HIS* 3.3 2.1 + - - +
409C LYS* 3.1 41.2 + - + +
416C PHE* 3.6 17.5 - + + -
421C TYR* 3.8 11.4 - - - +
501C NAP 3.7 22.4 - - - -
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Residues in contact with LYS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 3.4 23.0 + - - -
240C TYR* 4.9 6.3 + - - +
324C TRP* 4.9 6.1 - - - -
370C ALA* 4.8 15.9 - - + -
374C TYR* 3.9 17.5 - - + -
402C PHE 3.0 18.3 + - - +
403C LEU* 3.7 14.4 - - + +
404C GLU 3.3 0.2 - - - -
405C TRP* 1.3 108.4 - - + +
407C HIS* 1.3 61.9 + - - +
409C LYS* 3.1 33.8 + - + +
410C LYS* 3.1 16.9 + - - +
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Residues in contact with HIS 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C LEU 3.1 16.4 + - - +
404C GLU* 3.7 7.2 - - - +
406C LYS* 1.3 75.3 - - - +
408C HIS* 1.3 68.9 + - - +
410C LYS* 3.2 15.0 + - + +
411C GLU* 2.9 56.2 + - + +
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Residues in contact with HIS 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C GLU* 2.9 29.3 + - - +
405C TRP 3.7 5.2 - - - +
406C LYS 3.3 0.2 - - - -
407C HIS* 1.3 80.6 - - - +
409C LYS* 1.3 60.1 + - - +
411C GLU* 3.8 20.6 - - - +
412C ASN 3.3 23.7 + - - +
415C THR* 5.4 0.3 + - - -
416C PHE* 3.8 12.9 - - + +
419C HIS* 3.5 49.1 + + + -
420C SER 5.2 1.8 - - - -
421C TYR* 2.6 40.4 + + - +
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Residues in contact with LYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ASP* 5.3 0.6 + - - +
212C TYR* 3.9 22.4 - - - -
215C GLU* 2.9 29.8 + - - -
240C TYR* 3.5 30.1 + - + +
405C TRP* 3.1 37.5 + - + +
406C LYS* 3.1 23.5 + - + +
408C HIS* 1.3 75.2 - - - +
410C LYS* 1.3 65.1 + - - +
412C ASN 4.5 1.3 - - - -
413C ILE* 3.4 35.3 + - + +
416C PHE* 3.8 35.8 - - + -
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C MET 4.2 10.3 + - - -
239C GLY* 4.1 19.1 + - - -
240C TYR* 4.0 26.9 - - + +
241C LYS* 5.4 6.1 + - - +
406C LYS 3.1 11.7 + - - +
407C HIS* 3.4 19.1 - - + +
409C LYS* 1.3 77.0 - - - +
411C GLU* 1.3 66.2 + - - +
412C ASN* 4.4 0.3 - - - -
413C ILE 5.1 0.2 + - - -
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Residues in contact with GLU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 5.5 6.1 - - - +
407C HIS* 2.9 49.4 + - + +
408C HIS* 3.8 23.2 - - - +
409C LYS 3.3 0.2 - - - -
410C LYS* 1.3 79.2 - - - +
412C ASN* 1.3 65.1 + - + +
419C HIS* 4.3 12.3 + - - -
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Residues in contact with ASN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LYS* 5.0 6.3 - - - +
408C HIS 3.3 9.1 + - - +
409C LYS 3.6 3.4 - - - -
410C LYS 4.4 0.4 - - - -
411C GLU* 1.3 85.4 - - + +
413C ILE* 1.3 64.2 + - - +
414C MET* 3.0 20.2 + - - +
415C THR* 3.0 46.5 + - - +
416C PHE* 3.3 11.1 + - - +
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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
------------------------------------------------------------
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