Contacts of the helix formed by residues 439 - 457 (chain B) in PDB entry 3E4E
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 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 5.3 1.6 - - - -
437B CYS* 3.0 9.6 - - - -
438B ALA* 1.3 77.4 - - - +
440B GLU* 1.3 67.3 + - - +
441B GLY 3.4 2.5 - - - -
442B LEU* 3.2 8.9 + - - +
443B ALA* 2.9 21.2 + - - +
500B HEM 3.6 34.6 - - - +
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Residues in contact with GLU 440 (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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430B PHE* 3.6 38.2 - - + +
431B SER 5.0 0.7 - - - +
436B VAL* 3.7 22.6 - - + +
437B CYS* 3.4 14.2 + - - +
438B ALA 3.7 0.4 - - - -
439B GLY* 1.3 75.0 - - - +
441B GLY* 1.3 65.5 + - - +
443B ALA* 2.9 14.0 + - - +
444B ARG* 2.6 57.1 + - - +
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN* 5.3 1.3 - - - -
439B GLY 3.4 1.0 - - - -
440B GLU* 1.3 79.5 - - - +
442B LEU* 1.3 63.1 + - - +
444B ARG* 3.4 6.6 + - - +
445B MET* 3.1 28.1 + - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 5.9 2.2 - - + -
143B ASN* 3.6 39.6 - - - +
147B ILE* 3.9 14.6 - - + -
179B VAL* 4.0 10.1 - - + -
180B ILE* 4.5 7.2 - - + -
183B ILE* 4.2 19.3 - - + -
300B GLY 5.8 0.7 - - - +
439B GLY* 3.2 11.9 + - - +
441B GLY* 1.3 72.0 - - - +
443B ALA* 1.3 67.6 + - - +
445B MET* 2.9 6.3 + - - +
446B GLU* 2.7 50.3 + - - +
500B HEM 4.1 25.8 - - + -
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 4.2 11.0 - - - +
430B PHE* 3.6 27.1 - - + -
439B GLY 2.9 10.4 + - - +
440B GLU 2.9 9.7 + - - +
442B LEU* 1.3 75.1 - - - +
444B ARG* 1.3 57.5 + - - +
446B GLU* 3.0 8.3 + - - +
447B LEU* 2.9 33.7 + - + +
500B HEM 3.9 25.7 - - + +
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 3.3 21.6 + - - +
354B VAL* 5.1 2.6 - - + +
355B HIS* 3.0 33.3 + - - -
358B GLN* 5.1 6.1 - - - +
423B TYR* 6.2 2.0 - - - -
427B PHE* 3.5 22.7 - - - -
430B PHE* 3.7 20.1 - - + -
440B GLU* 2.6 58.0 + - - +
441B GLY* 4.0 5.4 - - - +
443B ALA* 1.3 73.5 - - - +
445B MET* 1.3 65.6 + - - +
447B LEU* 3.6 8.1 + - - +
448B PHE* 3.4 14.6 + - - +
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Residues in contact with MET 445 (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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137B GLY 6.0 0.9 - - - +
143B ASN* 3.8 19.5 - - + +
144B GLU* 3.3 37.5 - - + +
147B ILE* 3.7 9.2 - - + -
341B ILE* 3.6 34.1 - - + -
344B ARG* 4.4 7.2 - - - +
441B GLY 3.1 14.1 + - - +
442B LEU* 2.9 8.8 + - - +
444B ARG* 1.3 76.5 - - - +
446B GLU* 1.3 59.7 + - - +
448B PHE* 3.6 1.1 + - - +
449B LEU* 3.0 35.6 + - + +
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Residues in contact with GLU 446 (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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147B ILE* 3.6 26.0 - - + -
176B PRO* 3.8 16.7 - - - +
179B VAL* 3.2 30.3 - - + +
180B ILE* 5.7 0.2 - - - +
300B GLY 4.4 3.5 - - - +
304B THR* 3.2 35.2 + - + +
442B LEU* 2.7 29.2 + - - +
443B ALA* 3.0 9.9 + - - +
445B MET* 1.3 74.5 - - - +
447B LEU* 1.3 65.4 + - - +
450B LEU* 3.0 45.3 + - + +
500B HEM 5.1 0.9 - - - +
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 3.8 26.5 - - + +
307B THR* 3.6 33.0 - - + -
308B LEU* 4.0 16.0 - - + +
354B VAL* 4.0 18.3 - - + +
358B GLN* 3.5 36.1 - - - +
430B PHE* 5.0 0.2 - - + -
443B ALA* 2.9 27.1 + - + +
444B ARG* 3.6 4.5 + - - +
445B MET 3.4 0.2 - - - -
446B GLU* 1.3 72.2 - - - +
448B PHE* 1.3 57.2 + - - +
451B LEU* 3.1 33.3 + - + +
500B HEM 4.2 13.5 - - + -
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Residues in contact with PHE 448 (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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340B ALA 3.9 14.4 - - - -
341B ILE* 4.5 3.1 - - + -
343B ASP* 4.2 2.2 - - + -
344B ARG* 3.6 74.0 - - + +
347B MET* 4.1 11.0 - - + -
350B MET* 3.6 33.1 - - + +
351B ASP* 5.1 1.8 - - - -
354B VAL* 4.3 16.6 - - + -
444B ARG 3.4 5.9 + - - +
445B MET 4.2 1.1 - - - +
446B GLU 3.2 0.6 - - - -
447B LEU* 1.3 77.9 - - - +
449B LEU* 1.3 86.5 + - + +
451B LEU* 4.5 0.2 - - - +
452B CYS* 3.0 46.2 + - - +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU* 3.9 29.4 - - + +
147B ILE* 3.6 25.4 - - + -
148B GLN* 4.4 8.3 - - + +
151B ALA* 5.9 0.7 - - - -
339B PRO* 4.0 8.0 - - + +
340B ALA 3.6 16.8 - - - +
341B ILE* 3.6 22.2 - - - +
445B MET* 3.0 36.7 + - + +
448B PHE* 1.3 94.6 - - + +
450B LEU* 1.3 61.0 + - - +
452B CYS* 3.4 4.5 + - - +
453B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.0 17.5 - - + +
150B GLU* 5.7 0.7 - - + -
151B ALA* 3.9 31.2 - - + +
154B LEU* 3.8 23.1 - - + -
175B ALA* 4.1 19.7 - - + -
176B PRO* 4.9 4.5 - - + -
179B VAL* 6.0 2.0 - - + -
308B LEU* 4.4 23.8 - - + -
446B GLU* 3.0 39.4 + - + +
449B LEU* 1.3 76.2 - - - +
451B LEU* 1.3 59.8 + - - +
453B ALA* 3.5 1.8 - - + +
454B ILE* 2.9 37.0 + - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 4.6 10.9 - - + +
311B GLY* 5.8 1.3 - - - -
312B LEU* 4.1 26.0 - - + -
315B LEU* 4.2 9.6 - - + -
350B MET* 3.6 26.7 - - + -
353B VAL* 4.5 2.0 - - + -
354B VAL* 4.0 11.2 - - + -
357B ILE* 4.0 24.9 - - + -
447B LEU* 3.1 21.0 + - + +
448B PHE 4.5 0.4 - - - +
450B LEU* 1.3 78.2 - - - +
452B CYS* 1.3 63.7 + - - +
454B ILE* 4.0 6.9 - - + +
455B LEU* 3.2 47.1 + - + +
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Residues in contact with CYS 452 (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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329B ILE* 3.8 11.6 - - + +
333B ILE* 4.6 2.5 - - + -
339B PRO* 3.6 23.0 - - + +
347B MET* 4.2 16.8 - - - -
350B MET* 4.0 16.1 - - - -
448B PHE* 3.0 54.1 + - - +
449B LEU 3.4 4.5 - - - +
451B LEU* 1.3 78.6 - - - +
453B ALA* 1.3 62.7 + - - +
456B GLN* 3.0 25.6 + - - +
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Residues in contact with ALA 453 (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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151B ALA* 4.0 26.5 - - + -
154B LEU* 5.7 1.3 - - + -
155B LEU* 3.8 14.9 - - + +
338B ILE* 5.9 0.7 - - + -
339B PRO* 4.0 14.6 - - + +
449B LEU 2.9 17.5 + - - +
450B LEU* 3.5 7.0 - - + +
452B CYS* 1.3 72.9 - - - +
454B ILE* 1.3 68.1 + - + +
455B LEU 3.1 1.2 + - - -
456B GLN* 3.1 14.0 + - - -
457B HIS* 3.2 18.8 - - - -
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Residues in contact with ILE 454 (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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154B LEU* 4.1 19.7 - - + -
155B LEU* 4.0 7.6 - - - +
158B LEU* 3.9 26.0 - - + -
172B ILE* 4.4 14.8 - - + -
308B LEU* 5.0 8.1 - - + -
312B LEU* 4.7 19.1 - - + -
450B LEU* 2.9 30.0 + - + +
451B LEU* 4.0 7.4 - - + +
453B ALA* 1.3 77.1 - - - +
455B LEU* 1.3 65.7 + - + +
457B HIS 3.4 0.5 + - - -
458B PHE* 3.1 31.8 + - + +
460B LEU* 4.3 23.3 - - + -
489B VAL* 5.8 1.6 - - + -
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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
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315B LEU* 4.1 4.3 - - + -
322B GLU* 3.9 31.2 - - + +
325B LEU* 4.1 30.7 - - + -
326B HIS* 3.0 36.3 + - + -
329B ILE* 3.5 16.8 - - + -
350B MET* 4.8 1.8 - - - -
451B LEU* 3.2 42.3 + - + +
453B ALA 3.2 0.6 - - - -
454B ILE* 1.3 77.9 - - + +
456B GLN* 1.3 65.1 + - - +
457B HIS 3.1 3.3 + - - -
458B PHE 3.4 6.9 - - - +
460B LEU* 4.2 21.8 - - + -
492B ARG* 3.7 3.3 + - - -
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Residues in contact with GLN 456 (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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329B ILE* 3.8 19.4 - - + +
330B ASP* 5.3 1.3 - - - +
333B ILE* 3.5 7.0 - - - +
334B GLY 2.9 29.1 + - - +
335B PRO* 3.9 12.9 - - + +
336B SER 3.4 13.9 - - - +
337B ARG 3.2 23.6 + - - +
338B ILE* 4.5 2.3 - - - +
339B PRO* 3.4 22.0 - - - +
452B CYS 3.0 18.2 + - - +
453B ALA* 3.1 1.4 + - - +
455B LEU* 1.3 77.0 - - - +
457B HIS* 1.3 86.8 + - + +
492B ARG* 4.2 17.5 + - - +
493B SER* 5.4 1.9 + - - -
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Residues in contact with HIS 457 (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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155B LEU* 3.4 24.7 - - + +
159B ARG* 3.3 21.8 + - - +
335B PRO 4.2 13.2 + - - -
336B SER* 4.9 7.3 + - - -
338B ILE* 6.1 1.8 - - - +
453B ALA 3.2 17.3 - - - +
454B ILE 3.4 1.2 + - - -
455B LEU 3.1 0.4 - - - -
456B GLN* 1.3 108.8 + - + +
458B PHE* 1.3 88.9 + - + +
491B PRO* 3.3 4.3 - - - +
492B ARG* 2.8 26.7 + - - +
493B SER* 3.9 15.0 + - - +
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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
------------------------------------------------------------
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