Contacts of the helix formed by residues 403 - 421 (chain A) in PDB entry 5HAN
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 GLY 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ALA 3.7 6.4 - - - +
398A PHE* 5.6 0.9 - - - -
400A HIS* 3.1 11.9 + - - +
401A VAL 3.5 1.4 + - - -
402A ASP* 1.3 80.0 - - - +
404A GLY* 1.3 55.8 + - - -
405A ALA 3.3 2.7 - - - -
406A ALA* 3.3 2.5 + - - +
407A GLY* 2.8 31.9 + - - -
59B PHE* 5.7 2.9 - - - -
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP* 4.7 7.2 + - - +
184A PHE* 3.7 17.8 - - - -
397A ALA 3.9 11.4 + - - +
398A PHE* 4.2 25.7 - - - +
403A GLY* 1.3 68.7 - - - -
405A ALA* 1.3 59.2 + - - +
407A GLY* 3.4 0.7 + - - -
408A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP* 3.3 27.8 + - + +
184A PHE 4.5 0.9 - - - -
186A LEU* 4.1 20.6 - - + -
187A GLY* 4.1 3.2 - - - +
402A ASP 6.0 0.2 - - - +
403A GLY 3.3 1.0 - - - -
404A GLY* 1.3 74.6 - - - +
406A ALA* 1.3 57.9 + - - +
408A ALA* 3.3 8.2 + - - +
409A LYS* 3.0 39.6 + - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A HIS* 3.8 12.0 - - + -
402A ASP* 3.5 36.0 + - + +
403A GLY 3.3 7.0 + - - +
405A ALA* 1.3 75.1 - - - +
407A GLY* 1.3 59.2 + - - +
409A LYS* 3.3 3.0 + - - -
410A SER* 3.0 26.7 + - - -
433A GLU* 3.7 26.2 - - + +
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Residues in contact with GLY 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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396A GLY 4.5 0.2 - - - -
397A ALA* 3.7 18.1 - - - -
400A HIS* 3.6 23.6 - - - -
403A GLY 2.8 16.5 + - - -
404A GLY 3.4 2.7 + - - -
405A ALA 3.3 0.2 - - - -
406A ALA* 1.3 72.1 - - - +
408A ALA* 1.3 59.1 + - - +
410A SER* 2.5 25.3 + - - -
411A LEU* 3.3 10.9 + - - +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 3.5 10.4 - - - +
184A PHE* 3.3 35.7 - - + +
187A GLY 3.4 3.6 - - - +
188A GLY* 3.4 26.7 - - - +
404A GLY 2.9 10.9 + - - +
405A ALA 3.3 9.4 + - - +
407A GLY* 1.3 75.7 - - - +
409A LYS* 1.4 61.3 + - - +
411A LEU* 3.3 4.9 + - - -
412A ARG* 3.1 18.4 + - - +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.5 7.4 + - - -
187A GLY* 4.3 20.6 - - - +
405A ALA* 3.0 26.7 + - - +
406A ALA* 3.3 2.9 + - - +
408A ALA* 1.4 71.9 - - - +
410A SER* 1.4 61.5 + - - +
412A ARG* 3.5 8.2 - - + +
413A GLN* 2.8 44.9 + - - +
433A GLU* 3.7 41.0 + - + +
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Residues in contact with SER 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA* 3.5 21.9 - - - +
396A GLY 4.4 3.8 + - - -
400A HIS* 3.8 9.7 - - - -
406A ALA 3.0 11.3 + - - -
407A GLY* 2.5 25.7 + - - -
409A LYS* 1.4 74.9 - - - +
411A LEU* 1.3 59.8 + - - +
413A GLN* 3.7 2.0 - - - +
414A ALA* 2.8 30.1 + - - +
433A GLU* 3.5 21.7 - - - +
434A PHE* 3.8 15.2 - - - +
437A ALA* 4.1 2.0 - - - +
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Residues in contact with LEU 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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160A PHE* 3.9 6.8 - - + -
162A VAL* 4.0 15.3 - - + -
163A GLY 3.6 24.2 - - - +
184A PHE* 4.4 4.9 - - + -
373A ASN* 4.0 2.7 - - - -
374A ALA* 3.7 18.2 - - - +
377A MET* 3.2 48.5 - - + +
391A MET* 5.7 1.6 - - + +
393A ALA* 3.9 26.7 - - + -
396A GLY 4.8 3.8 - - - +
397A ALA* 4.5 5.8 - - + -
407A GLY 3.4 14.1 - - - +
408A ALA* 3.3 10.0 + - - +
409A LYS 3.2 0.4 - - - -
410A SER* 1.3 76.7 - - - +
412A ARG* 1.3 63.9 + - - +
414A ALA 3.2 0.9 + - - -
415A GLU 3.2 7.4 + - - -
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Residues in contact with ARG 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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153A ARG* 3.5 14.5 - - - +
160A PHE* 4.4 3.1 + - - -
162A VAL* 3.4 26.0 - - + +
187A GLY 3.2 23.0 + - - -
188A GLY* 3.8 7.1 - - - -
189A ASP* 2.9 42.2 + - - -
225A GLU* 4.7 9.5 + - - -
408A ALA 3.1 13.8 + - - +
409A LYS* 3.5 13.2 - - + +
411A LEU* 1.3 74.1 - - - +
413A GLN* 1.3 66.2 + - + +
415A GLU* 3.3 6.2 + - - +
416A GLN* 3.1 48.7 + - - +
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Residues in contact with GLN 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 LYS* 2.8 26.4 + - + +
410A SER 3.7 4.0 - - - +
412A ARG* 1.3 80.2 - - + +
414A ALA* 1.3 56.7 + - - +
416A GLN* 3.0 19.0 + - - +
417A CYS 2.9 26.2 + - - -
427A PHE* 3.4 12.7 - - + -
431A HIS* 3.3 27.1 - - + +
433A GLU* 3.0 29.4 + - - +
434A PHE* 2.9 39.2 + - + +
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Residues in contact with ALA 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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374A ALA* 3.2 32.1 - - - +
377A MET* 3.9 12.8 - - + -
378A PRO* 4.4 7.7 - - + +
381A PHE* 5.0 1.3 - - - -
410A SER 2.8 21.2 + - - +
411A LEU 3.2 5.6 + - - +
413A GLN* 1.3 74.6 - - - +
415A GLU* 1.4 60.6 + - - +
417A CYS* 3.4 7.5 + - - +
418A TRP* 3.2 20.8 + - - +
434A PHE* 3.9 14.1 - - + -
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Residues in contact with GLU 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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159A GLY* 5.7 0.5 - - - -
160A PHE* 3.4 50.8 + - + +
377A MET* 3.9 0.8 - - - +
381A PHE* 3.8 17.9 - - + -
387A SER* 2.7 32.4 + - - -
411A LEU 3.2 7.3 + - - -
412A ARG 4.0 3.2 - - - +
414A ALA* 1.4 72.2 - - - +
416A GLN* 1.3 70.5 + - - +
418A TRP* 3.3 2.9 + - + +
419A LYS* 2.7 46.4 + - - +
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Residues in contact with GLN 416 (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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412A ARG* 3.1 36.0 + - + +
413A GLN* 3.0 26.7 + - - +
415A GLU* 1.3 81.7 - - - +
417A CYS* 1.3 60.0 + - - +
419A LYS* 3.3 5.2 + - - -
420A GLN* 2.8 54.6 + - - +
427A PHE* 4.3 6.9 - - + -
431A HIS* 4.9 4.3 + - - -
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Residues in contact with CYS 417 (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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378A PRO* 5.3 2.9 - - + -
413A GLN 2.9 8.7 + - - +
414A ALA* 3.4 13.9 - - - +
416A GLN* 1.3 74.8 - - - +
418A TRP* 1.3 63.6 + - - +
420A GLN 3.2 2.4 + - - -
421A GLY 3.1 3.6 + - - -
422A ALA* 3.1 48.5 + - - +
424A PRO* 3.7 22.2 - - - -
427A PHE* 3.5 50.6 - - + -
434A PHE* 4.6 2.7 - - + -
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Residues in contact with TRP 418 (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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378A PRO* 3.6 26.5 - - + -
381A PHE* 3.3 42.8 - + + -
382A ASP* 2.8 33.9 + - - +
385A GLY* 3.9 10.3 - - - -
386A HIS* 3.7 24.5 - - - -
387A SER* 3.6 28.9 - - - -
414A ALA 3.2 10.2 + - - +
415A GLU* 3.6 7.9 - - - +
416A GLN 3.3 0.2 - - - -
417A CYS* 1.3 80.0 - - - +
419A LYS* 1.3 86.2 + - + +
421A GLY* 3.1 14.5 + - - +
422A ALA 5.3 0.9 - - - +
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Residues in contact with LYS 419 (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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386A HIS* 6.1 0.8 - - - +
387A SER* 4.1 12.8 + - - +
388A ASN* 5.8 4.4 + - - +
415A GLU* 2.7 41.9 + - - +
416A GLN* 3.7 8.5 - - - +
418A TRP* 1.3 86.3 - - + +
420A GLN* 1.4 60.4 + - + +
421A GLY 3.8 0.3 + - - -
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Residues in contact with GLN 420 (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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416A GLN* 2.8 40.6 + - - +
417A CYS 3.8 4.0 - - - +
418A TRP 3.1 0.4 - - - -
419A LYS* 1.4 78.5 - - + +
421A GLY* 1.3 62.8 + - - +
422A ALA* 3.5 7.8 + - + +
427A PHE* 3.5 22.9 - - - -
431A HIS* 5.5 0.9 + - - -
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Residues in contact with GLY 421 (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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417A CYS 3.1 0.6 + - - -
418A TRP* 3.1 15.5 + - - -
419A LYS 3.5 0.8 + - - -
420A GLN* 1.3 77.3 - - - +
422A ALA* 1.3 61.4 + - - +
423A ASP 4.2 0.2 + - - -
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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