Contacts of the helix formed by residues 452 - 470 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 4.6 4.9 - - - -
450B CYS* 3.2 9.2 - - - -
451B LEU* 1.3 77.2 - - - +
453B ARG* 1.3 66.0 + - - +
454B ARG 3.1 3.4 + - - -
455B LEU* 3.2 7.5 + - - +
456B ALA* 2.8 24.4 + - - +
601B HEM 3.7 36.9 - - - +
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Residues in contact with ARG 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.1 8.6 - - + +
366B ARG* 3.8 2.2 - - - +
440B HIS* 5.6 2.4 + - - -
443B PHE* 3.6 43.0 - - + -
449B GLN* 4.6 21.7 - - - +
450B CYS* 3.4 26.8 - - + +
451B LEU 3.3 2.4 + - - -
452B GLY* 1.3 77.9 - - - +
454B ARG* 1.3 95.0 + - - +
456B ALA* 3.9 1.1 - - - +
457B GLU* 3.0 54.8 + - - +
603B SO4 2.9 37.5 + - - -
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.6 57.4 + - + +
150B SER* 4.1 0.2 - - - +
151B PRO* 3.8 26.9 - - - +
154B VAL* 3.3 34.5 - - + +
157B PHE* 4.3 4.8 - - + -
359B THR* 6.6 0.2 - - - -
449B GLN* 6.0 0.8 - - - +
451B LEU 5.0 0.2 + - - -
452B GLY 3.2 0.6 - - - -
453B ARG* 1.3 91.8 - - - +
455B LEU* 1.3 61.2 + - - +
457B GLU* 3.9 5.0 - - - +
458B ALA* 2.9 30.8 + - - +
603B SO4 2.6 42.1 + - - +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 5.0 6.5 + - + +
157B PHE* 3.8 30.3 - - + -
161B VAL* 4.1 8.1 - - + -
200B SER* 4.9 4.5 - - - +
203B ALA* 3.6 32.1 - - + -
204B LEU* 4.6 12.3 - - + -
289B ILE* 4.5 13.0 - - + -
315B SER* 5.0 2.0 - - - -
452B GLY* 3.2 12.4 + - - +
454B ARG* 1.3 74.5 - - - +
456B ALA* 1.3 68.3 + - - +
458B ALA* 3.0 4.5 + - - +
459B GLU* 2.9 46.7 + - - +
601B HEM 4.0 22.9 - - + -
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Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B THR* 3.7 22.6 - - - +
443B PHE* 4.6 2.5 - - + -
452B GLY 2.8 20.3 + - - +
453B ARG* 3.9 5.2 - - - +
455B LEU* 1.3 74.0 - - - +
457B GLU* 1.3 59.7 + - - +
459B GLU* 3.2 6.1 + - - +
460B MET* 2.8 33.4 + - - +
601B HEM 3.9 36.3 - - + +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ARG* 3.2 31.4 + - - +
369B LEU* 4.4 12.9 - - + +
440B HIS* 4.5 7.6 + - - -
443B PHE* 3.3 30.9 - - + -
453B ARG* 3.0 46.4 + - - +
454B ARG* 3.9 5.5 - - - +
456B ALA* 1.3 74.4 - - - +
458B ALA* 1.3 59.2 + - - +
460B MET* 4.1 7.7 - - - +
461B LEU* 2.9 35.2 + - + +
603B SO4 4.2 3.6 + - - -
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 5.5 2.0 - - + -
157B PHE* 4.5 12.6 - - + -
158B LEU* 4.1 28.5 - - + -
161B VAL* 4.1 10.5 - - + -
359B THR* 6.1 3.1 - - + -
454B ARG 2.9 18.9 + - - +
455B LEU* 3.4 6.7 - - - +
457B GLU* 1.3 76.4 - - - +
459B GLU* 1.3 62.6 + - - +
461B LEU* 4.6 5.2 - - - -
462B LEU* 2.9 30.5 + - - +
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Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 3.8 12.8 - - + -
195B TYR* 2.6 37.5 + - + +
196B THR* 4.0 8.0 - - - -
199B ALA* 3.5 21.9 - - + -
200B SER* 2.7 42.7 + - - -
315B SER* 4.0 5.5 - - - +
319B THR* 3.7 23.2 + - + +
323B LEU* 4.7 0.2 - - - -
455B LEU* 2.9 34.6 + - + +
456B ALA* 3.6 7.2 - - - +
458B ALA* 1.3 71.7 - - - +
460B MET* 1.3 63.7 + - - +
463B LEU* 3.3 8.8 + - - +
601B HEM 6.1 0.9 - - - -
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Residues in contact with MET 460 (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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319B THR* 3.3 19.1 - - + +
322B PRO* 3.2 21.3 - - + -
323B LEU* 3.0 52.6 - - + +
369B LEU* 3.8 28.5 - - + -
373B LEU* 5.1 7.0 - - - -
443B PHE* 5.8 0.2 - - - -
456B ALA 2.8 27.1 + - - +
457B GLU* 4.3 4.9 - - - -
459B GLU* 1.3 75.1 - - - +
461B LEU* 1.3 65.5 + - - +
463B LEU 3.5 0.2 + - - -
464B LEU* 3.2 30.7 + - - +
601B HEM 4.1 18.8 - - - -
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA* 3.6 35.0 - - + +
359B THR* 4.0 15.0 - - + +
362B LEU* 4.4 10.1 - - + +
365B LEU* 3.7 32.4 - - + +
366B ARG* 3.7 33.0 - - + +
369B LEU* 4.3 9.8 - - + +
457B GLU* 2.9 20.3 + - + +
458B ALA* 4.0 4.9 - - - +
460B MET* 1.3 76.8 - - - +
462B LEU* 1.3 59.6 + - + +
464B LEU* 3.7 4.1 - - - +
465B HIS* 2.9 30.3 + - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 2.9 33.9 - - + -
161B VAL* 3.3 13.7 - - + -
162B ASP* 3.2 48.7 - - + +
165B ALA* 3.7 13.7 - - + -
351B ILE* 4.9 3.4 - - + -
355B PRO 4.9 2.2 - - - +
358B ALA* 4.1 26.0 - - + -
458B ALA* 2.9 15.0 + - - +
461B LEU* 1.3 78.0 - - + +
463B LEU* 1.3 66.4 + - - +
465B HIS* 3.3 6.1 + - + +
466B HIS* 3.0 31.3 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 3.7 10.2 - - - +
168B PHE* 3.8 21.3 - - + -
169B SER* 4.7 0.3 + - - -
192B ILE* 3.8 28.9 - - + -
195B TYR* 3.1 44.6 - - + -
323B LEU* 4.4 14.8 - - + -
327B LEU* 4.9 6.1 - - + -
459B GLU 3.3 17.8 + - - +
460B MET 4.1 2.5 - - - +
462B LEU* 1.3 77.7 - - - +
464B LEU* 1.3 71.3 + - + +
466B HIS* 3.9 2.5 - - - +
467B VAL* 3.0 37.7 + - + +
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Residues in contact with LEU 464 (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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323B LEU* 3.8 18.6 - - + -
326B THR* 4.0 20.0 - - + -
327B LEU* 3.8 30.7 - - + -
330B LEU* 4.8 8.7 - - + -
365B LEU* 3.8 24.2 - - + -
369B LEU* 3.5 30.5 - - + -
460B MET 3.2 18.7 + - - +
461B LEU* 3.7 3.1 - - - +
463B LEU* 1.3 79.5 - - + +
465B HIS* 1.3 64.8 + - - +
467B VAL* 3.1 5.0 + - + +
468B LEU* 2.8 31.1 + - + +
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Residues in contact with HIS 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B SER* 3.2 47.9 + - - -
348B ALA* 4.2 4.4 + - - -
351B ILE* 3.6 36.1 - - + +
362B LEU* 3.5 20.6 - - + +
365B LEU* 3.7 7.3 - - + +
461B LEU 2.9 17.7 + - - +
462B LEU* 3.3 8.5 + - + +
464B LEU* 1.3 77.7 - - - +
466B HIS* 1.3 87.1 + + - +
468B LEU* 3.2 3.4 + - - +
469B LYS* 3.1 42.9 + - + +
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Residues in contact with HIS 466 (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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162B ASP* 2.8 27.7 + - - -
165B ALA* 3.8 23.6 - - + +
166B ARG* 3.2 34.7 - - + +
169B SER* 3.3 16.9 + - - +
351B ILE* 5.4 3.8 - - + -
352B SER* 6.1 4.3 - - - -
462B LEU* 3.0 27.4 + - + +
463B LEU 4.1 1.3 - - - +
465B HIS* 1.3 92.2 - + - +
467B VAL* 1.3 63.9 + - - +
469B LYS* 3.7 28.2 + - - +
470B HIS* 2.9 31.2 + - + +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 4.2 16.4 - - + -
169B SER* 3.5 15.0 - - - +
172B LEU* 4.8 1.3 - - + -
327B LEU* 4.5 9.9 - - + -
463B LEU* 3.0 33.4 + - + +
464B LEU* 3.6 6.3 - - + +
466B HIS* 1.3 77.3 - - - +
468B LEU* 1.3 66.0 + - + +
470B HIS 3.2 1.2 + - - -
471B PHE* 2.9 38.3 + - + +
473B VAL* 4.1 15.7 - - + -
499B PHE* 4.1 28.9 - - + -
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Residues in contact with LEU 468 (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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330B LEU* 4.3 15.3 - - + -
337B GLN* 4.0 26.2 - - + +
340B LEU* 3.9 24.2 - - + +
341B ARG* 3.3 52.2 + - - +
344B SER* 4.0 21.5 - - - +
365B LEU* 4.0 20.0 - - + -
464B LEU* 2.8 23.0 + - + +
465B HIS 3.2 4.7 + - - +
467B VAL* 1.3 80.5 - - + +
469B LYS* 1.3 65.0 + - - +
471B PHE 4.0 3.8 - - - +
473B VAL* 5.6 1.8 - - + -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B SER* 4.1 13.7 - - - +
345B LEU* 4.0 26.9 - - + +
348B ALA* 3.5 36.0 + - + +
352B SER* 5.3 8.5 - - - -
465B HIS* 3.1 25.2 + - + +
466B HIS* 3.7 32.1 + - - +
467B VAL 3.4 0.4 - - - -
468B LEU* 1.3 77.4 - - - +
470B HIS* 1.3 85.8 + - + +
471B PHE 3.8 0.2 - - - -
502B ILE* 3.6 11.8 - - - +
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Residues in contact with HIS 470 (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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169B SER* 4.4 11.0 - - - -
173B LYS* 3.6 39.9 + - + +
466B HIS* 2.9 25.0 + - - +
467B VAL 3.2 2.0 + - - -
469B LYS* 1.3 108.6 + - + +
471B PHE* 1.3 81.4 + + + +
501B ALA* 3.6 5.7 - - - -
502B ILE* 3.2 26.9 + - - +
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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