Contacts of the helix formed by residues 397 - 411 (chain B) in PDB entry 4D2Y
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B ARG* 3.6 25.3 - - - +
383B GLU* 4.3 16.7 + - - -
395B GLN 5.3 0.7 - - - +
396B LEU* 1.3 76.8 - - - +
398B ASP* 1.3 61.3 + - - +
399B THR* 3.2 14.8 - - + +
400B GLU* 2.9 32.7 + - - +
401B LEU* 2.9 26.5 + - - +
430B ARG* 4.4 0.4 - - - -
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU 4.8 0.2 - - - +
397B LYS* 1.3 72.9 - - - +
399B THR* 1.3 60.5 - - + +
401B LEU* 3.3 4.3 + - - +
402B ILE* 3.0 40.4 + - + +
428B ASP* 3.5 12.9 - - + +
430B ARG* 3.2 20.9 + - - +
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Residues in contact with THR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B TYR* 3.2 28.5 + - - +
397B LYS* 3.8 12.8 - - - +
398B ASP* 1.3 77.9 - - + +
400B GLU* 1.3 60.3 + - - +
402B ILE* 3.5 11.1 + - + +
403B TYR* 3.0 28.9 + - - +
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 3.5 24.0 - - + -
362B LEU* 3.4 19.7 - - + +
365B TYR* 3.9 26.8 - - + -
366B TYR* 4.4 6.4 + - - -
380B ARG* 2.7 51.5 + - - +
396B LEU* 3.6 11.4 - - + +
397B LYS* 2.9 25.9 + - + +
399B THR* 1.3 80.1 + - - +
401B LEU* 1.3 55.1 + - - +
403B TYR* 3.5 5.2 - - - +
404B GLY* 2.7 31.4 + - - -
574B ILE* 4.7 0.2 - - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.9 18.0 - - + +
397B LYS 2.9 13.4 + - - +
398B ASP* 3.3 10.5 + - - +
400B GLU* 1.3 76.3 - - - +
402B ILE* 1.3 56.8 + - + +
404B GLY* 3.1 1.7 + - - -
405B ALA* 2.9 29.9 + - - +
426B VAL* 4.6 6.1 - - + -
428B ASP* 3.9 21.1 - - + +
430B ARG* 3.7 28.7 - - - +
461B ILE* 3.9 33.0 - - + -
574B ILE* 4.1 8.3 - - + -
579B PHE* 3.9 28.0 - - + -
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP* 3.0 31.4 + - + +
399B THR* 3.8 9.6 - - + +
401B LEU* 1.3 74.0 - - + +
403B TYR* 1.3 65.5 + - - +
405B ALA* 3.3 1.9 + - - +
406B LYS* 3.0 52.5 + - + +
424B LEU 5.6 0.2 - - - +
426B VAL* 4.0 33.2 - - + +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 3.6 29.2 - + - -
364B GLN* 3.6 31.3 + - - +
365B TYR* 3.7 31.9 - + + -
368B SER* 3.2 30.8 - - - -
369B ILE* 6.0 0.2 - - + -
399B THR 3.0 17.3 + - - +
400B GLU 3.5 2.9 - - - +
402B ILE* 1.3 78.1 - - - +
404B GLY* 1.3 58.6 + - - +
406B LYS* 3.5 4.8 + - - +
407B HIS* 3.0 82.8 + + + +
702B PRO* 5.0 0.4 - - + -
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Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 4.0 17.3 - - - -
400B GLU 2.7 20.1 + - - -
401B LEU 3.5 1.3 - - - -
403B TYR* 1.3 74.8 - - - +
405B ALA* 1.3 56.7 + - - +
407B HIS 3.3 0.5 + - - -
408B ALA* 3.0 26.0 + - - +
574B ILE* 3.7 17.0 - - - +
702B PRO* 3.3 15.2 - - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B LEU 2.9 15.8 + - - +
402B ILE 3.3 3.8 + - - +
404B GLY* 1.3 72.9 - - - +
406B LYS* 1.3 66.4 + - - +
408B ALA* 3.3 5.1 + - - +
409B TRP* 3.2 21.3 + - - +
424B LEU* 3.9 9.7 - - + +
426B VAL* 4.0 16.2 - - + -
459B ILE* 4.2 7.0 - - + -
461B ILE* 4.0 23.8 - - + -
572B LEU* 4.5 8.3 - - + -
574B ILE* 3.9 5.1 - - - +
704B PHE* 4.5 3.6 - - - -
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 3.0 40.8 + - + +
403B TYR* 3.8 5.4 - - - +
405B ALA* 1.3 76.2 - - - +
407B HIS* 1.3 59.1 + - + +
409B TRP* 3.3 4.6 + - - +
410B ARG* 2.9 25.6 + - - +
421B TRP* 3.5 35.3 - - + +
422B SER* 3.1 30.3 + - - +
424B LEU* 3.6 37.3 + - + +
426B VAL* 4.8 0.7 - - + -
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Residues in contact with HIS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLN* 5.3 1.8 + - - -
368B SER* 5.3 2.4 - - - -
403B TYR* 3.0 71.9 + + + +
404B GLY 4.0 2.9 - - - +
405B ALA 3.1 0.2 - - - -
406B LYS* 1.3 77.7 - - + +
408B ALA* 1.3 59.6 + - - +
410B ARG* 3.1 41.8 - - - +
411B ASN* 2.8 39.6 + - - +
421B TRP* 3.7 20.3 - + - -
669B ARG* 3.9 12.3 + - - -
702B PRO* 4.1 17.9 - - + -
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B GLY 3.0 12.2 + - - +
405B ALA 3.3 4.5 + - - +
407B HIS* 1.3 75.2 - - - +
409B TRP* 1.3 63.0 + - - +
411B ASN* 3.3 3.1 + - - +
412B ALA* 3.2 21.8 + - - +
572B LEU* 3.4 32.5 - - + -
702B PRO* 3.3 12.9 + - - +
703B SER* 3.7 15.9 - - - +
704B PHE* 3.7 17.1 + - + -
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Residues in contact with TRP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B ALA 3.2 7.2 + - - +
406B LYS* 3.5 7.0 - - - +
407B HIS 3.2 0.2 - - - -
408B ALA* 1.3 81.3 - - - +
410B ARG* 1.3 63.5 + - - +
412B ALA* 3.0 12.7 + - - +
415B CYS* 3.4 11.2 - - + -
417B GLY 3.6 18.4 - - - -
418B ARG* 3.1 18.5 - - + +
420B GLN* 3.4 35.9 - - + -
421B TRP* 3.4 21.1 - - + -
423B LYS 3.7 12.1 - - - -
424B LEU* 3.9 11.9 - - + -
457B SER* 3.7 10.8 - - - -
704B PHE* 3.6 7.5 - - - -
750B HEM 3.3 91.8 + + + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B LYS 2.9 14.6 + - - +
407B HIS* 3.1 38.7 + - - +
409B TRP* 1.3 77.2 - - - +
411B ASN* 1.3 58.3 + - - +
418B ARG* 3.2 24.2 + - - +
421B TRP* 3.3 53.4 - - + +
661B HIS* 5.1 2.5 + - + -
665B GLU* 2.8 43.6 + - - +
668B CYS* 3.7 16.6 - - - -
669B ARG* 3.7 37.9 + - - +
672B CYS* 5.5 0.9 - - - -
673B PRO* 5.1 0.9 - - - +
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B HIS* 2.8 20.6 + - - +
408B ALA 3.3 2.4 + - - +
409B TRP 3.0 0.4 - - - -
410B ARG* 1.3 75.9 - - - +
412B ALA* 1.3 60.0 + - - +
413B SER* 2.9 10.6 + - - -
418B ARG* 4.0 3.6 - - - +
669B ARG* 2.8 39.0 + - - +
673B PRO* 4.1 12.8 - - - +
698B TYR 5.2 2.4 - - - +
699B ARG* 6.0 0.2 - - - -
700B LEU* 3.5 35.8 + - + +
701B THR 3.5 12.9 + - - -
702B PRO* 3.0 29.4 + - - +
703B SER* 5.3 1.7 - - - -
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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