Contacts of the helix formed by residues 397 - 411 (chain A) in PDB entry 2HX4
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 LYS 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ARG* 3.4 36.0 - - - +
383A GLU* 3.9 21.0 + - - -
395A GLN 5.6 0.4 - - - +
396A LEU* 1.3 81.6 - - - +
398A ASP* 1.3 67.1 + - - +
399A THR* 3.4 14.1 - - + +
400A GLU* 2.8 23.7 + - - +
401A LEU* 3.2 16.5 + - - +
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Residues in contact with ASP 398 (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 LEU 4.8 0.2 - - - +
397A LYS* 1.3 72.2 - - - +
399A THR* 1.3 69.0 + - + +
401A LEU* 3.0 15.7 + - - +
402A ILE* 3.0 25.0 + - + +
428A ASP* 3.8 8.4 - - - +
430A ARG* 3.4 20.8 + - - +
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Residues in contact with THR 399 (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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365A TYR* 3.3 27.8 + - - +
397A LYS* 3.7 13.9 - - + +
398A ASP* 1.3 79.8 - - + +
400A GLU* 1.3 58.7 + - - +
402A ILE* 3.5 9.7 + - - +
403A TYR* 3.0 28.4 + - - +
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Residues in contact with GLU 400 (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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361A PHE* 3.5 18.9 - - + -
362A LEU* 3.8 12.9 - - - +
365A TYR* 4.1 23.2 - - + -
366A TYR* 5.1 1.2 + - - -
380A ARG* 2.8 52.1 + - - +
394A TYR* 5.2 0.2 - - - -
396A LEU* 3.3 25.8 - - + +
397A LYS* 2.8 28.2 + - + +
398A ASP 3.1 0.4 - - - -
399A THR* 1.3 82.9 + - - +
401A LEU* 1.3 61.0 + - - +
403A TYR* 4.4 4.0 - - - -
404A GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 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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396A LEU* 4.1 13.4 - - + +
397A LYS 3.2 12.7 + - - +
398A ASP* 3.0 10.4 + - - +
400A GLU* 1.3 76.4 - - - +
402A ILE* 1.3 59.0 + - + +
404A GLY* 3.9 0.3 - - - -
405A ALA* 3.0 28.5 + - - +
426A VAL* 4.6 6.1 - - + -
428A ASP* 3.6 23.8 - - + +
430A ARG* 3.6 33.9 - - - +
461A ILE* 3.5 42.0 - - + -
574A ILE* 4.0 5.1 - - + +
579A PHE* 4.1 19.7 - - + -
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Residues in contact with ILE 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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398A ASP* 3.0 24.9 + - + +
399A THR* 3.8 7.6 - - - +
401A LEU* 1.3 77.1 - - + +
403A TYR* 1.3 64.6 + - - +
405A ALA* 4.0 0.7 - - - +
406A LYS* 3.0 51.6 + - + +
426A VAL* 4.0 33.4 - - + +
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Residues in contact with TYR 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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361A PHE* 3.3 33.0 - + - -
364A GLN* 3.1 41.3 + - + +
365A TYR* 3.6 24.2 - + + -
368A SER* 3.4 33.2 - - - -
399A THR 3.0 18.0 + - - +
400A GLU 3.9 2.0 - - - +
402A ILE* 1.3 77.9 - - - +
404A GLY* 1.3 58.5 + - - +
406A LYS* 3.9 4.4 - - - +
407A HIS* 3.0 75.5 + + + +
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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
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400A GLU 2.9 17.9 + - - -
403A TYR* 1.3 81.8 - - - +
405A ALA* 1.3 57.0 + - - +
407A HIS 3.3 1.0 + - - -
408A ALA* 2.9 25.1 + - - +
574A ILE* 3.7 20.6 - - - -
702A PRO* 3.3 27.1 - - - +
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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
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401A LEU 3.0 18.5 + - - +
402A ILE 4.0 3.1 - - - +
404A GLY* 1.3 71.1 - - - +
406A LYS* 1.3 67.9 + - - +
408A ALA* 3.1 13.5 + - - +
409A TRP* 3.3 9.5 + - - +
424A LEU* 3.9 20.1 - - + +
426A VAL* 4.2 8.7 - - + -
459A ILE* 4.4 6.7 - - + -
461A ILE* 4.0 21.5 - - + -
572A LEU* 4.4 10.1 - - + -
574A ILE* 3.7 4.9 - - - +
704A PHE* 4.4 2.8 - - - -
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Residues in contact with LYS 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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402A ILE* 3.0 41.6 + - + +
403A TYR* 3.9 5.6 - - - +
405A ALA* 1.3 75.6 - - - +
407A HIS* 1.3 59.7 + - - +
409A TRP* 3.4 5.4 + - - +
410A ARG* 2.9 24.9 + - - +
421A TRP* 3.4 26.9 - - + +
422A SER* 3.1 31.1 + - - +
423A LYS 5.2 0.2 - - - -
424A LEU* 3.5 42.7 + - + -
426A VAL* 4.9 1.3 - - + -
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Residues in contact with HIS 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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364A GLN* 4.4 4.3 - - - -
368A SER* 5.6 0.6 - - - -
403A TYR* 3.0 70.6 + + + +
404A GLY 3.9 3.1 - - - +
406A LYS* 1.3 77.0 - - - +
408A ALA* 1.3 59.9 + - - +
409A TRP 3.2 0.4 - - - -
410A ARG* 3.0 34.2 + - - +
411A ASN* 2.8 37.4 + - - +
421A TRP* 3.6 27.6 - + - -
669A ARG* 4.0 15.0 - - - -
702A PRO* 4.0 17.3 - - + -
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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
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404A GLY 2.9 12.7 + - - +
405A ALA 3.1 2.4 + - - +
407A HIS* 1.3 77.5 - - - +
409A TRP* 1.3 62.3 + - - +
411A ASN* 3.4 3.5 + - - +
412A ALA* 3.2 17.3 + - - +
572A LEU* 3.2 35.0 - - + -
702A PRO 3.4 12.1 + - - -
703A SER* 3.7 19.0 - - - +
704A PHE* 3.5 20.3 + - + -
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Residues in contact with TRP 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 ALA 3.3 6.7 + - - +
406A LYS 3.6 7.2 - - - +
407A HIS 3.2 0.2 - - - -
408A ALA* 1.3 77.3 - - - +
410A ARG* 1.3 64.9 + - - +
412A ALA* 3.0 13.1 + - - +
415A CYS* 3.5 10.6 - - - -
417A GLY 3.7 15.9 - - - -
418A ARG* 3.0 19.8 - - + +
420A GLN* 3.5 34.3 - - + -
421A TRP* 3.5 25.4 - - + -
424A LEU* 3.7 15.9 - - + -
457A SER* 3.5 25.6 - - - -
704A PHE* 3.5 7.8 - - - -
750A HEM 3.3 82.6 + + + -
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Residues in contact with ARG 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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406A LYS 2.9 15.4 + - - +
407A HIS* 3.0 45.9 + - - +
409A TRP* 1.3 77.6 - - - +
411A ASN* 1.3 58.3 + - - +
418A ARG* 3.0 25.8 + - - +
421A TRP* 3.4 50.6 - - + +
661A HIS* 5.1 2.2 + - + -
665A GLU* 3.0 41.3 + - - +
668A CYS* 5.3 6.7 - - - +
669A ARG* 3.8 36.3 + - - +
672A CYS* 5.3 0.7 - - - -
673A PRO* 4.8 1.2 - - - +
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Residues in contact with ASN 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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364A GLN* 5.6 0.2 - - - +
407A HIS* 2.8 18.4 + - - +
408A ALA 3.4 2.7 + - - +
409A TRP 3.1 0.2 - - - -
410A ARG* 1.3 78.6 - - - +
412A ALA* 1.3 58.0 + - - +
413A SER* 2.8 12.4 + - - -
418A ARG* 3.9 2.5 - - - +
669A ARG* 2.9 39.3 + - - +
673A PRO* 4.0 10.6 - - + +
698A TYR 5.3 1.7 - - - +
699A ARG* 6.0 0.3 - - - -
700A LEU* 3.7 29.4 + - + +
701A THR 3.6 17.2 + - - -
702A PRO* 2.8 30.7 + - - +
703A SER* 5.1 4.3 - - - -
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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