Contacts of the helix formed by residues 400 - 415 (chain A) in PDB entry 1H23
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 VAL 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A SER* 3.7 41.7 - - - +
227A GLY 4.4 0.6 + - - +
231A CYS* 4.7 5.0 - - - -
233A TRP* 4.8 2.2 - - + +
288A PHE* 3.8 25.6 - - + -
323A VAL* 4.2 7.4 - - + -
327A GLU* 3.7 33.9 - - + +
396A GLY* 3.0 9.7 + - - +
398A HIS 3.7 0.6 - - - -
399A ASN* 1.3 86.0 - - + +
401A ILE* 1.3 66.9 + - - +
403A PRO* 3.4 3.5 - - - +
404A LEU* 3.0 26.7 + - + +
440A HIS* 4.3 5.4 - - + -
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A VAL* 3.9 33.2 - - + -
324A ASN 4.0 17.0 - - - +
325A LYS 4.9 6.5 - - - +
327A GLU* 4.4 7.4 - - + -
396A GLY* 2.9 20.3 + - - +
397A ASP* 3.9 19.7 - - - +
400A VAL* 1.3 70.8 - - - +
402A CYS* 1.3 58.9 + - - +
404A LEU* 3.1 4.0 + - - +
405A MET* 2.9 41.0 + - + +
422A PHE* 4.7 6.1 - - + -
516A LEU* 4.7 5.4 - - + -
517A ARG* 4.0 26.5 - - + -
521A CYS* 4.2 9.0 - - - -
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Residues in contact with CYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASP* 2.8 35.4 + - - +
401A ILE* 1.3 75.4 - - - +
403A PRO* 1.3 63.5 - - + +
405A MET* 3.9 0.4 - - - +
406A HIS* 3.1 17.5 + - - +
520A MET 4.0 0.4 - - - -
521A CYS* 2.0 58.8 - - + -
524A TRP* 3.7 22.9 - - + -
525A ASN* 3.1 27.1 + - - +
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Residues in contact with PRO 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER* 3.6 1.8 - - - -
230A ASN* 2.8 36.1 + - - +
231A CYS* 3.9 25.4 - - - -
232A PRO* 3.6 16.4 - - + -
397A ASP 3.3 4.0 - - - +
398A HIS 3.1 28.5 - - - +
399A ASN 3.9 4.5 - - - +
400A VAL 3.4 10.1 - - - +
402A CYS* 1.3 90.9 - - + +
404A LEU* 1.3 62.0 + - - +
406A HIS* 3.3 2.0 + - + -
407A PHE 3.0 10.9 + - - -
525A ASN* 4.7 3.4 - - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU 4.6 0.7 - - - +
226A SER 4.5 0.7 - - - +
227A GLY 3.8 26.2 - - - +
228A SER* 3.5 15.0 + - - +
321A LEU* 4.0 24.7 - - + -
322A GLY* 3.6 25.4 - - - +
323A VAL* 3.8 17.3 - - + -
400A VAL 3.0 20.0 + - - +
401A ILE 3.6 2.2 - - - +
403A PRO* 1.3 78.5 - - - +
405A MET* 1.3 65.7 + - - +
407A PHE* 3.1 2.3 + - - +
408A VAL* 2.8 27.1 + - + +
420A LEU* 3.9 27.1 - - + -
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Residues in contact with MET 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 2.9 29.8 + - + +
402A CYS* 3.9 6.7 - - - +
403A PRO 3.3 0.2 - - - -
404A LEU* 1.3 86.1 - - - +
406A HIS* 1.3 62.4 + - - +
408A VAL* 3.1 20.7 - - + +
409A ASN* 3.1 43.0 + - - +
420A LEU* 3.9 22.7 - - + -
495A PHE* 4.3 6.7 - - + -
500A GLN* 5.7 1.3 - - + +
515A ARG* 5.3 1.8 - - - -
516A LEU* 3.9 50.0 - - + +
521A CYS* 4.3 11.9 - - + -
525A ASN* 4.8 1.3 - - - +
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Residues in contact with HIS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASN* 3.7 18.4 - - + +
306A GLU* 2.8 39.4 + - - -
309A LEU* 4.6 5.8 - - + -
402A CYS 3.1 16.8 + - - +
403A PRO* 3.6 4.3 - - + +
405A MET* 1.3 78.7 - - - +
407A PHE* 1.3 62.4 + - - +
409A ASN* 3.5 4.2 + - - +
410A LYS* 3.1 49.2 + - + +
525A ASN* 3.6 28.9 + - + +
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Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLY* 4.7 4.3 - - - -
210A ILE* 4.5 17.5 - - + -
211A LEU* 5.3 2.0 - - + -
224A LEU* 4.0 22.9 - - + -
228A SER* 4.1 10.5 - - - -
229A PRO* 3.7 30.1 - - + -
230A ASN* 3.5 19.9 - - - +
309A LEU* 3.8 27.1 - - + -
319A ILE* 4.1 14.6 - - + -
321A LEU* 3.9 21.8 - - + -
403A PRO 3.0 8.3 + - - +
404A LEU 3.6 5.2 - - - +
406A HIS* 1.3 79.8 - - - +
408A VAL* 1.3 59.4 + - - +
410A LYS* 3.3 4.4 + - - +
411A TYR* 2.8 48.8 + + + +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ILE* 4.9 0.9 - - + -
321A LEU* 4.3 18.6 - - + -
404A LEU* 2.8 21.8 + - + +
405A MET* 3.1 42.0 - - + +
407A PHE* 1.3 80.1 - - - +
409A ASN* 1.3 56.4 + - - +
411A TYR* 4.5 2.9 - - - -
412A THR* 2.7 39.8 + - - +
418A THR* 3.4 32.8 - - + -
420A LEU* 4.8 3.8 - - + -
495A PHE* 3.8 18.2 - - + -
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Residues in contact with ASN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A MET* 3.1 38.1 + - - +
406A HIS* 4.1 4.2 - - - +
408A VAL* 1.3 78.7 - - - +
410A LYS* 1.3 65.8 + - + +
412A THR* 3.7 1.7 + - - -
413A LYS* 3.7 15.9 + - - +
495A PHE* 3.5 27.3 - - - -
497A THR* 4.8 11.1 + - - +
500A GLN* 3.9 22.6 + - - +
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A GLU* 3.8 6.7 + - - -
309A LEU* 4.2 32.6 - - + +
310A ASN* 2.3 33.8 + - - +
314A PHE* 4.0 10.2 - - - -
406A HIS* 3.1 50.6 + - + +
407A PHE 3.9 2.7 - - - +
409A ASN* 1.3 79.9 - - + +
411A TYR* 1.3 63.0 + - - +
413A LYS* 3.5 16.5 + - - +
414A PHE* 4.1 4.2 - - - -
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Residues in contact with TYR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.8 13.0 - - + +
309A LEU* 5.2 1.1 - - - +
314A PHE* 3.3 32.8 - + - -
315A LYS 2.7 28.7 + - - -
317A THR* 2.8 42.9 + - - +
319A ILE* 3.5 43.5 - - + -
407A PHE* 2.8 40.3 + + + +
408A VAL 4.0 2.5 - - - +
410A LYS* 1.3 75.6 - - - +
412A THR* 1.3 55.4 + - - +
414A PHE* 2.9 8.1 + - - +
415A GLY* 2.8 43.7 + - - -
416A ASN 4.7 0.2 - - - -
417A GLY 5.1 0.4 - - - -
418A THR* 4.3 5.2 - - - -
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A VAL* 2.7 23.5 + - - +
409A ASN 4.1 3.1 - - - -
411A TYR* 1.3 74.7 - - - +
413A LYS* 1.3 66.6 + - - +
414A PHE 3.2 1.0 + - - -
415A GLY* 3.7 12.6 + - - +
418A THR* 2.8 24.7 + - - +
495A PHE* 3.4 36.4 - - + +
496A THR* 4.2 1.3 - - - -
497A THR* 3.8 25.9 + - - +
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ASN 3.7 9.9 + - - +
410A LYS* 3.5 14.7 + - + +
411A TYR 3.1 0.4 - - - -
412A THR* 1.3 79.5 - - - +
414A PHE* 1.3 80.7 + - + +
497A THR* 4.2 13.2 + - + +
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU 4.3 3.6 - - - -
310A ASN 3.9 13.0 - - - -
311A SER* 4.0 7.6 - - - -
312A GLY* 3.6 37.2 - - - -
314A PHE* 3.9 23.8 - + + -
316A LYS* 3.7 36.6 - - + +
410A LYS 4.1 3.8 - - - -
411A TYR 2.9 2.8 + - - -
413A LYS* 1.3 100.7 - - + +
415A GLY* 1.3 63.2 + - - +
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Residues in contact with GLY 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PHE* 4.8 0.2 - - - -
316A LYS* 4.6 5.8 - - - -
317A THR 4.0 0.9 - - - -
411A TYR* 2.8 41.4 + - - -
412A THR* 3.7 9.9 + - - +
414A PHE* 1.3 76.5 - - - +
416A ASN* 1.3 62.5 + - - -
417A GLY 3.4 3.4 + - - -
418A THR* 5.9 0.4 - - - -
1538A NAG 3.9 7.1 - - - +
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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