Contacts of the helix formed by residues 452 - 469 (chain L) in PDB entry 4DVQ
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 452 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 4.6 5.2 - - - -
450L CYS* 3.3 7.5 - - - -
451L LEU* 1.3 78.0 - - - +
453L ARG* 1.3 63.2 + - - +
454L ARG 3.4 2.0 - - - -
455L LEU* 3.2 8.7 + - - +
456L ALA* 2.9 22.9 + - - +
601L HEM 3.5 39.5 - - - +
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Residues in contact with ARG 453 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L LEU* 4.3 6.9 - - + +
366L ARG* 5.6 0.8 - - - +
443L PHE* 3.5 46.8 - - + -
449L GLN* 3.8 23.7 + - - -
450L CYS* 3.2 23.6 - - + +
451L LEU 3.4 3.0 + - - -
452L GLY* 1.3 76.8 - - - +
454L ARG* 1.3 89.1 + - - +
456L ALA* 3.3 3.6 + - - +
457L GLU* 2.9 46.0 + - - +
603L SO4 2.7 44.3 + - - -
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Residues in contact with ARG 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L VAL 5.2 0.4 - - - +
149L LEU* 2.7 57.7 + - + +
150L SER 4.8 1.6 - - - -
151L PRO* 4.1 22.7 - - - +
154L VAL* 3.6 27.8 - - + +
157L PHE* 4.6 2.9 - - - -
452L GLY 3.4 0.6 - - - -
453L ARG* 1.3 97.5 - - - +
455L LEU* 1.3 60.8 + - - +
457L GLU* 3.9 6.3 - - - +
458L ALA* 2.9 30.3 + - - +
603L SO4 3.2 47.6 + - - +
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Residues in contact with LEU 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L VAL* 4.9 7.6 + - + +
157L PHE* 3.4 35.6 - - + -
161L VAL* 4.2 7.0 - - + -
200L SER* 4.6 6.5 - - - +
203L ALA* 3.5 25.8 - - + -
204L LEU* 4.7 10.5 - - + -
289L ILE* 4.3 18.2 - - + -
315L SER* 5.1 1.8 - - - -
452L GLY* 3.2 10.8 + - - +
454L ARG* 1.3 78.2 - - - +
456L ALA* 1.3 57.9 + - - +
458L ALA* 3.2 3.3 + - - +
459L GLU* 2.9 54.4 + - - +
601L HEM 4.0 22.9 - - + -
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Residues in contact with ALA 456 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L THR* 3.8 22.2 - - - +
443L PHE* 4.6 0.7 - - + -
452L GLY 2.9 16.8 + - - +
453L ARG* 3.4 6.7 - - - +
455L LEU* 1.3 78.3 - - - +
457L GLU* 1.3 56.9 - - - +
459L GLU* 3.4 5.2 + - - +
460L MET* 3.0 36.5 + - - +
601L HEM 3.9 36.7 - - + +
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Residues in contact with GLU 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366L ARG* 4.0 28.5 + - - +
369L LEU* 4.5 16.0 - - + +
370L LYS* 5.5 2.9 + - - +
373L LEU* 5.6 0.8 - - + +
440L HIS* 5.3 4.9 + - - -
443L PHE* 3.8 23.3 - - + -
453L ARG* 2.9 56.5 + - - +
454L ARG* 4.0 6.0 - - - +
455L LEU 3.3 0.2 - - - -
456L ALA* 1.3 73.4 - - - +
458L ALA* 1.3 60.0 + - - +
460L MET* 4.1 5.3 - - - +
461L LEU* 2.9 34.6 + - - +
603L SO4 4.0 5.5 + - - -
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Residues in contact with ALA 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L VAL* 4.9 2.2 - - + -
157L PHE* 4.6 10.3 - - + -
158L LEU* 4.2 28.7 - - + -
161L VAL* 4.0 5.2 - - + -
454L ARG 2.9 19.3 + - - +
455L LEU* 3.6 6.7 - - - +
457L GLU* 1.3 75.4 - - - +
459L GLU* 1.3 63.0 + - - +
461L LEU* 4.6 4.9 - - - -
462L LEU* 3.1 37.8 + - + +
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Residues in contact with GLU 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L VAL* 3.8 10.5 - - + -
195L TYR* 2.7 35.2 + - + +
196L THR* 4.0 11.1 - - - -
199L ALA* 3.8 19.4 - - + -
200L SER* 2.7 39.5 + - - -
315L SER* 5.9 0.4 - - - -
319L THR* 3.7 26.8 + - + +
455L LEU* 2.9 39.4 + - + +
456L ALA* 3.7 4.7 - - - +
458L ALA* 1.3 77.2 - - - +
460L MET* 1.3 61.7 + - - +
463L LEU* 3.4 9.0 + - - +
601L HEM 6.1 0.4 - - - -
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Residues in contact with MET 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319L THR* 3.6 20.0 - - + +
322L PRO* 3.2 33.9 - - + -
323L LEU* 3.4 29.4 - - + +
326L THR* 4.5 0.2 - - - +
369L LEU* 3.6 38.4 - - + -
372L THR* 5.4 0.7 - - + -
373L LEU* 5.1 6.7 - - + -
456L ALA 3.0 22.0 + - - +
457L GLU* 4.1 3.4 - - - +
459L GLU* 1.3 75.3 - - - +
461L LEU* 1.3 64.4 + - - +
463L LEU* 4.1 0.9 - - - +
464L LEU* 3.2 31.8 + - + +
601L HEM 4.1 22.7 - - + -
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Residues in contact with LEU 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358L ALA* 3.2 39.0 - - + +
359L THR* 4.1 7.2 - - - +
362L LEU* 4.1 12.6 - - + -
365L LEU* 3.7 29.2 - - + +
366L ARG* 3.9 37.5 - - + +
369L LEU* 4.2 10.2 - - + +
457L GLU 2.9 20.5 + - - +
458L ALA* 4.0 4.7 - - - +
460L MET* 1.3 77.9 - - - +
462L LEU* 1.3 58.7 + - + +
464L LEU* 4.7 2.2 - - - -
465L HIS* 2.9 28.6 + - - +
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Residues in contact with LEU 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158L LEU* 3.4 38.1 - - + +
161L VAL* 3.3 23.8 - - + -
162L ASP* 3.9 21.1 - - + +
165L ALA* 3.6 15.3 - - + -
351L ILE* 5.3 3.6 - - + -
355L PRO* 4.5 2.2 - - + +
358L ALA* 3.8 28.5 - - + -
458L ALA* 3.1 22.4 + - + +
461L LEU* 1.3 78.6 - - + +
463L LEU* 1.3 66.5 + - - +
465L HIS* 3.4 6.3 + - + +
466L HIS* 3.1 30.6 + - + +
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Residues in contact with LEU 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L ALA* 3.7 11.7 - - - +
168L PHE* 3.3 43.7 - - + -
169L SER* 4.7 0.3 + - - -
192L ILE* 3.8 13.0 - - + -
195L TYR* 3.7 26.7 - - + -
323L LEU* 3.1 38.1 - - + -
327L LEU* 4.7 3.8 - - + -
459L GLU 3.4 16.7 + - - +
460L MET 4.1 1.8 - - - +
462L LEU* 1.3 76.9 - - - +
464L LEU* 1.3 68.8 + - + +
466L HIS* 3.0 5.3 + - - +
467L VAL* 2.9 31.4 + - + +
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Residues in contact with LEU 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323L LEU* 3.9 19.3 - - + -
326L THR* 3.6 34.3 - - + -
327L LEU* 4.0 29.4 - - + -
330L LEU* 4.8 9.6 - - + -
365L LEU* 3.9 22.9 - - + -
369L LEU* 4.1 16.8 - - + -
460L MET* 3.2 19.7 + - + +
461L LEU 3.7 3.1 - - - +
463L LEU* 1.3 82.9 - - + +
465L HIS* 1.3 63.5 + - - +
467L VAL* 3.4 4.9 + - + +
468L LEU* 3.1 31.4 + - + +
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Residues in contact with HIS 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344L SER* 2.8 59.3 + - - -
348L ALA* 4.1 6.9 - - - -
351L ILE* 3.3 44.4 - - + +
362L LEU* 3.9 18.1 - - + +
365L LEU* 3.7 3.3 - - + +
461L LEU 2.9 18.2 + - - +
462L LEU* 3.7 11.0 - - + +
463L LEU 3.2 0.2 - - - -
464L LEU* 1.3 77.2 - - - +
466L HIS* 1.3 77.2 + + - +
468L LEU* 3.6 0.3 + - - +
469L LYS* 3.4 32.7 + - + +
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Residues in contact with HIS 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L ASP* 2.9 27.0 + - - -
165L ALA* 3.8 21.1 - - + +
166L ARG* 3.5 45.3 + - + +
169L SER* 3.4 17.3 - - - +
351L ILE* 5.1 2.6 - - + +
462L LEU* 3.1 20.6 + - - +
463L LEU 3.0 7.1 + - - +
465L HIS* 1.3 89.9 - + - +
467L VAL* 1.3 66.4 + - - +
469L LYS* 3.5 28.2 + - - +
470L HIS* 3.0 30.4 + - + -
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Residues in contact with VAL 467 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L PHE* 4.3 15.9 - - + -
169L SER* 3.8 12.1 - - - +
172L LEU* 5.3 0.9 - - + -
327L LEU* 4.5 9.9 - - + -
463L LEU* 2.9 36.4 + - + +
464L LEU* 3.9 6.5 - - + +
466L HIS* 1.3 77.5 - - - +
468L LEU* 1.3 61.6 + - + +
470L HIS 3.1 1.6 + - - -
471L PHE* 2.9 39.5 + - + +
473L VAL* 4.1 16.8 - - + -
499L PHE* 4.0 29.2 - - + -
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Residues in contact with LEU 468 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330L LEU* 4.1 14.8 - - + -
337L GLN* 3.8 36.3 - - + +
340L LEU* 3.7 27.1 - - + -
341L ARG* 3.2 46.1 + - - +
344L SER* 4.2 13.9 - - - +
365L LEU* 4.0 20.6 - - + -
464L LEU* 3.1 22.2 + - + +
465L HIS 3.9 4.0 - - - +
466L HIS 3.3 0.2 - - - -
467L VAL* 1.3 84.8 - - + +
469L LYS* 1.3 58.6 + - - +
470L HIS 3.2 1.0 + - - -
471L PHE 3.6 5.5 - - - +
473L VAL* 5.4 1.8 - - + -
502L ILE* 4.0 0.3 - - - +
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Residues in contact with LYS 469 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG* 4.6 10.2 - - - +
341L ARG* 4.9 0.7 - - - -
344L SER* 4.7 7.4 - - - -
345L LEU* 3.8 32.6 - - + +
348L ALA* 4.0 28.2 - - + +
352L SER* 4.8 7.1 + - - -
465L HIS* 3.4 24.6 + - + +
466L HIS* 3.5 35.0 - - - +
467L VAL 3.2 1.0 - - - -
468L LEU* 1.3 77.3 - - - +
470L HIS* 1.3 89.4 + - + +
502L ILE* 5.0 6.2 - - - +
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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
------------------------------------------------------------
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