Contacts of the helix formed by residues 409 - 426 (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 SER 409 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370D VAL* 3.8 19.6 - - - +
374D ILE* 4.0 0.7 - - - +
406D PHE* 3.1 16.0 + - - +
407D LYS 3.1 1.3 - - - -
408D VAL* 1.3 81.0 - - - +
410D GLN* 1.3 63.6 + - - +
411D VAL* 3.6 9.4 + - - +
412D ILE* 3.1 42.5 + - - +
413D MET* 3.0 19.2 + - - +
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Residues in contact with GLN 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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407D LYS 4.5 3.2 + - - -
408D VAL 4.2 0.8 - - - -
409D SER* 1.3 70.7 - - - +
411D VAL* 1.3 60.6 + - + +
413D MET* 3.4 12.9 + - - +
414D GLU* 2.9 59.3 + - + +
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D ILE* 3.6 27.8 - - + -
409D SER* 3.2 3.4 + - - +
410D GLN* 1.3 79.7 - - + +
412D ILE* 1.3 62.4 + - - +
414D GLU* 3.4 14.1 + - - +
415D LYS* 3.0 56.4 + - + +
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Residues in contact with ILE 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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363D LEU* 3.9 3.8 - - + -
370D VAL* 3.9 12.6 - - + +
373D CYS* 3.8 29.6 - - + -
374D ILE* 3.5 18.8 - - + -
377D LEU* 4.1 11.2 - - + +
403D ILE* 3.8 37.0 - - + +
406D PHE* 3.8 33.4 - - + -
409D SER* 3.1 26.9 + - - +
411D VAL* 1.3 76.6 - - - +
413D MET* 1.3 53.2 + - - +
416D SER* 2.8 38.3 + - - -
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Residues in contact with MET 413 (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 ILE 3.9 1.3 - - - +
404D ARG 3.1 24.9 - - - +
405D ARG* 4.3 2.7 - - + -
406D PHE 3.1 32.1 - - - +
407D LYS* 3.6 36.6 - - + +
409D SER 3.0 10.5 + - - +
410D GLN* 3.5 14.1 - - - +
411D VAL 3.4 0.2 - - - -
412D ILE* 1.3 75.9 - - - +
414D GLU* 1.3 59.4 + - + +
416D SER* 3.4 4.6 + - - -
417D THR* 2.7 34.1 + - - -
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Residues in contact with GLU 414 (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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410D GLN* 2.9 53.1 + - + +
411D VAL* 3.7 14.3 - - - +
413D MET* 1.3 74.5 - - + +
415D LYS* 1.3 64.7 + - + +
417D THR* 3.8 4.3 - - - -
418D MET* 3.1 23.4 + - - +
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Residues in contact with LYS 415 (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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374D ILE* 4.0 11.0 - - + -
377D LEU* 4.0 25.1 - - + -
378D ASP* 2.9 30.1 + - - +
411D VAL* 3.0 40.8 + - + +
412D ILE* 4.7 0.2 - - - -
414D GLU* 1.3 78.2 - - + +
416D SER* 1.3 58.0 + - - +
418D MET* 3.4 21.5 + - + +
419D LEU* 2.9 31.4 + - - +
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Residues in contact with SER 416 (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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377D LEU* 4.4 4.2 - - - +
400D LEU* 3.7 16.5 - - - +
403D ILE* 3.4 29.5 + - - -
404D ARG* 3.3 25.9 + - - +
412D ILE 2.8 23.8 + - - -
413D MET 3.4 0.2 + - - -
415D LYS* 1.3 73.6 - - - +
417D THR* 1.3 58.1 + - - +
419D LEU* 3.8 6.1 - - - +
420D TYR* 2.7 36.4 + - - +
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Residues in contact with THR 417 (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 ARG* 3.4 34.7 + - + +
413D MET 2.7 25.0 + - - -
414D GLU* 3.8 4.9 - - - -
416D SER* 1.3 77.2 + - - +
418D MET* 1.3 56.7 + - - +
420D TYR* 4.0 0.8 - - - +
421D ASN* 2.9 53.6 + - - +
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Residues in contact with MET 418 (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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377D LEU 5.5 0.2 - - - +
381D ALA* 4.1 16.4 - - + -
414D GLU 3.1 16.2 + - - +
415D LYS* 3.4 29.4 - - + +
417D THR* 1.3 77.3 - - - +
419D LEU* 1.3 80.9 + - + +
421D ASN* 3.9 6.6 - - - +
422D LYS* 3.1 41.0 + - - +
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Residues in contact with LEU 419 (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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377D LEU* 3.4 48.7 - - + +
380D LEU* 4.0 18.8 - - + +
381D ALA* 3.8 21.8 - - + +
400D LEU* 4.0 9.6 - - + -
415D LYS* 2.9 20.2 + - + +
416D SER* 3.8 4.3 - - - +
418D MET* 1.3 95.9 - - + +
420D TYR* 1.3 67.5 + - - +
422D LYS* 3.3 20.9 - - - +
423D PHE* 3.1 34.0 + - + -
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Residues in contact with TYR 420 (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* 3.7 34.3 - - + -
400D LEU* 4.1 14.9 - - + +
401D LYS* 3.6 44.0 + - + +
404D ARG* 3.7 35.0 - - - -
416D SER 2.7 22.7 + - - +
417D THR 4.0 1.6 - - - +
419D LEU* 1.3 73.2 - - - +
421D ASN* 1.3 62.0 + - - +
423D PHE* 3.2 4.8 + - - +
424D LYS* 2.9 66.2 + - + +
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Residues in contact with ASN 421 (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 ARG* 5.1 3.5 + - - -
417D THR* 2.9 38.6 + - - +
418D MET* 3.9 6.9 - - - +
420D TYR* 1.3 80.3 - - - +
422D LYS* 1.3 58.2 + - - +
424D LYS* 3.2 20.7 + - - +
425D ASN* 2.9 49.2 + - - +
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Residues in contact with LYS 422 (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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380D LEU 4.3 3.8 + - - -
381D ALA* 3.5 35.8 + - - +
383D LEU 4.5 8.2 + - - -
418D MET* 3.1 26.7 + - - +
419D LEU* 3.3 21.7 - - + +
421D ASN* 1.3 79.8 - - - +
423D PHE* 1.3 72.6 - - + +
425D ASN* 4.1 3.8 - - - +
426D MET* 3.2 35.8 + - + +
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Residues in contact with PHE 423 (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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380D LEU* 3.9 31.9 - - + -
385D VAL* 3.8 32.8 - - + -
390D ALA* 4.3 11.3 - - + +
396D MET* 4.7 7.2 - - + -
397D ILE* 4.5 28.2 - - + +
400D LEU* 3.9 26.9 - - + -
419D LEU* 3.1 28.9 + - + +
420D TYR 3.8 3.1 - - - +
421D ASN 3.2 0.2 - - - -
422D LYS* 1.3 91.7 - - + +
424D LYS* 1.3 64.8 + - - +
426D MET* 3.3 38.8 - - + +
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Residues in contact with LYS 424 (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* 5.6 2.4 - - + +
404D ARG* 5.3 2.8 - - - +
420D TYR* 2.9 51.7 + - + +
421D ASN* 3.2 28.5 + - - +
423D PHE* 1.3 76.3 - - - +
425D ASN* 1.3 76.8 + - - +
426D MET 3.2 4.8 + - - -
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Residues in contact with ASN 425 (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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421D ASN* 2.9 37.4 + - - +
422D LYS* 4.2 4.2 - - - +
424D LYS* 1.3 86.0 - - - +
426D MET* 1.3 63.3 + - - +
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Residues in contact with MET 426 (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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385D VAL* 3.3 27.6 - - + +
386D THR 3.8 17.9 - - - +
387D MET* 3.4 50.8 - - + +
390D ALA* 4.4 4.5 - - - -
422D LYS* 3.2 33.7 + - + +
423D PHE* 3.3 43.3 - - + +
424D LYS 3.2 6.0 - - - -
425D ASN* 1.3 81.2 - - - +
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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