Contacts of the helix formed by residues 439 - 457 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 5.4 0.4 - - - -
437A CYS* 3.0 6.2 - - - -
438A ALA* 1.3 80.1 - - - +
440A GLU* 1.3 70.2 + - - +
441A GLY 3.2 2.8 + - - -
442A LEU* 3.2 7.8 + - - +
443A ALA* 2.9 26.0 + - - +
500A HEM 3.7 33.8 - - - +
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Residues in contact with GLU 440 (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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427A PHE* 5.9 0.2 - - - -
430A PHE* 3.7 39.1 - - + +
431A SER 4.8 1.7 - - - +
436A VAL* 3.5 23.2 - - - +
437A CYS* 3.9 12.2 + - - +
438A ALA 3.7 1.2 - - - -
439A GLY* 1.3 77.2 - - - +
441A GLY* 1.3 65.7 + - - +
443A ALA* 3.2 0.7 + - - +
444A ARG* 2.7 63.7 + - - +
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Residues in contact with GLY 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 5.3 0.7 - - - -
439A GLY 3.3 0.6 - - - -
440A GLU* 1.3 81.3 - - - +
442A LEU* 1.3 63.2 + - - +
444A ARG* 3.1 6.0 + - - +
445A MET* 2.9 29.7 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 5.9 1.8 - - + -
143A ASN* 3.6 39.8 - - + +
147A ILE* 3.9 13.2 - - + -
179A VAL* 3.8 18.6 - - + -
180A ILE* 5.2 7.9 - - + -
183A ILE* 4.2 14.6 - - + -
300A GLY 5.5 0.4 - - - +
439A GLY* 3.2 10.3 + - - +
441A GLY* 1.3 73.3 - - - +
443A ALA* 1.4 51.3 + - - +
445A MET* 3.2 5.0 + - - +
446A GLU* 2.7 61.2 + - - +
500A HEM 4.3 25.6 - - + -
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Residues in contact with ALA 443 (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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304A THR* 4.5 2.9 - - + +
430A PHE* 3.5 25.4 - - + -
439A GLY 2.9 16.4 + - - +
440A GLU 3.4 4.5 - - - +
442A LEU* 1.4 74.5 - - - +
444A ARG* 1.3 59.8 + - - +
446A GLU* 3.0 15.6 + - - +
447A LEU* 2.9 34.3 + - - +
500A HEM 4.0 26.4 - - + +
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Residues in contact with ARG 444 (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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344A ARG* 3.6 24.4 + - - +
354A VAL* 5.1 1.9 - - + +
355A HIS* 3.4 29.9 + - - -
358A GLN* 4.8 6.8 - - - +
423A TYR* 5.8 6.9 - - - -
427A PHE* 3.5 24.4 - - - -
430A PHE* 3.6 18.8 - - + -
440A GLU* 2.7 53.3 + - - +
441A GLY* 3.7 5.2 - - - +
443A ALA* 1.3 74.2 - - - +
445A MET* 1.3 65.4 + - - +
447A LEU* 4.1 8.2 - - - +
448A PHE* 3.5 15.8 + - - +
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Residues in contact with MET 445 (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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137A GLY 6.0 0.7 - - - +
143A ASN* 3.7 23.3 - - + +
144A GLU* 3.7 35.4 - - + +
147A ILE* 3.7 12.3 - - + -
341A ILE* 3.7 37.2 - - + -
344A ARG* 5.2 1.8 - - - +
441A GLY* 2.9 15.8 + - - +
442A LEU* 3.6 8.1 - - - +
444A ARG* 1.3 78.7 - - - +
446A GLU* 1.3 61.5 + - - +
448A PHE* 4.2 1.2 - - - +
449A LEU* 3.2 29.6 + - + +
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Residues in contact with GLU 446 (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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147A ILE* 3.7 26.0 - - + -
176A PRO* 4.0 15.0 - - - +
179A VAL* 3.2 32.4 - - + +
300A GLY 4.7 2.4 - - - +
304A THR* 3.2 33.4 + - + +
308A LEU* 5.5 0.4 - - - -
442A LEU* 2.7 34.6 + - - +
443A ALA* 3.3 9.6 - - - +
445A MET* 1.3 71.6 - - - +
447A LEU* 1.3 66.8 + - - +
450A LEU* 3.0 40.2 + - + +
500A HEM 4.7 0.7 - - - +
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Residues in contact with LEU 447 (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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304A THR* 3.6 25.1 - - + -
307A THR* 3.8 28.0 - - + -
308A LEU* 4.1 20.3 - - + +
354A VAL* 3.9 16.8 - - + +
358A GLN* 3.3 44.6 - - + +
430A PHE* 5.1 0.2 - - + -
443A ALA 2.9 21.6 + - - +
444A ARG* 4.1 4.7 - - - +
445A MET 3.4 0.2 - - - -
446A GLU* 1.3 75.3 - - - +
448A PHE* 1.3 56.7 + - - +
451A LEU* 2.9 34.5 + - - +
500A HEM 4.5 9.9 - - + -
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Residues in contact with PHE 448 (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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340A ALA 4.0 20.6 - - - -
341A ILE* 4.7 2.7 - - + -
343A ASP* 4.1 1.8 - - + -
344A ARG* 3.5 66.4 - - + +
347A MET* 4.0 12.3 - - + -
350A MET* 3.6 35.0 - - + +
351A ASP* 4.7 4.9 - - - -
354A VAL* 4.1 16.8 - - + +
444A ARG 3.5 14.2 + - - +
445A MET* 4.4 1.6 - - - +
446A GLU 3.3 0.8 - - - -
447A LEU* 1.3 76.8 - - - +
449A LEU* 1.3 75.3 + - + +
452A CYS* 2.8 51.1 + - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 3.9 24.0 - - + +
147A ILE* 3.7 30.5 - - + -
148A GLN* 4.6 5.6 - - + +
151A ALA* 6.0 0.4 - - - -
339A PRO* 3.8 9.4 - - + +
340A ALA* 3.5 43.1 - - - +
341A ILE* 3.6 3.1 - - + +
445A MET* 3.2 34.7 + - + +
448A PHE* 1.3 85.4 - - + +
450A LEU* 1.3 57.5 + - + +
452A CYS* 3.2 5.0 + - - +
453A ALA* 2.7 36.6 + - - +
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Residues in contact with LEU 450 (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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147A ILE* 3.7 25.6 - - + +
150A GLU* 5.9 1.6 - - + -
151A ALA* 4.3 18.2 - - + +
154A LEU* 3.7 21.3 - - + -
175A ALA* 3.9 24.7 - - + -
176A PRO* 4.4 7.4 - - + -
179A VAL* 6.2 1.6 - - + -
308A LEU* 4.1 26.7 - - + -
446A GLU* 3.0 32.1 + - + +
449A LEU* 1.3 78.8 - - + +
451A LEU* 1.3 62.9 + - - +
453A ALA* 3.3 2.5 + - + +
454A ILE* 3.1 31.2 + - + +
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Residues in contact with LEU 451 (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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308A LEU* 4.2 11.6 - - + +
311A GLY* 5.8 1.3 - - - -
312A LEU* 4.2 20.0 - - + -
315A LEU* 3.9 13.7 - - + -
350A MET* 3.4 23.7 - - + +
353A VAL* 4.4 7.6 - - + -
354A VAL* 3.9 14.4 - - + -
357A ILE* 4.1 24.5 - - + -
447A LEU 2.9 22.3 + - - +
450A LEU* 1.3 77.9 - - - +
452A CYS* 1.3 60.4 + - - +
454A ILE* 4.2 5.8 - - + -
455A LEU* 3.3 41.7 + - + +
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Residues in contact with CYS 452 (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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329A ILE* 4.2 7.9 - - - +
333A ILE* 4.7 2.7 - - + -
339A PRO* 3.7 23.1 - - + +
347A MET* 3.9 20.4 - - - -
350A MET* 3.4 14.5 - - - +
448A PHE* 2.8 53.3 + - - +
449A LEU 3.2 5.2 - - - +
451A LEU* 1.3 75.5 - - - +
453A ALA* 1.3 66.2 + - - +
455A LEU* 3.4 1.2 + - - +
456A GLN* 2.9 26.0 + - - +
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Residues in contact with ALA 453 (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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151A ALA* 4.1 25.6 - - + -
154A LEU* 5.6 2.5 - - + -
155A LEU* 3.9 17.7 - - + -
338A ILE* 5.6 0.4 - - + -
339A PRO* 3.9 14.5 - - + +
449A LEU 2.7 19.9 + - - +
450A LEU* 3.6 6.1 - - + +
452A CYS* 1.3 72.7 - - - +
454A ILE* 1.3 71.8 + - + +
456A GLN* 3.0 19.6 + - - +
457A HIS* 3.3 8.4 - - - -
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Residues in contact with ILE 454 (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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154A LEU* 4.5 18.4 - - + -
155A LEU* 3.9 8.9 - - + +
158A LEU* 4.1 24.2 - - + -
172A ILE* 5.2 8.3 - - + -
308A LEU* 4.8 10.8 - - + -
312A LEU* 4.6 23.6 - - + -
450A LEU* 3.1 23.7 + - + +
451A LEU* 4.1 8.1 - - + +
453A ALA* 1.3 80.4 - - - +
455A LEU* 1.3 69.0 + - + +
457A HIS 3.2 1.2 + - - -
458A PHE* 3.1 28.8 + - + +
460A LEU* 4.3 22.9 - - + -
489A VAL* 5.7 1.3 - - + -
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Residues in contact with LEU 455 (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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315A LEU* 3.8 13.5 - - + -
322A GLU* 4.2 7.4 - - + +
325A LEU* 4.1 26.2 - - + -
326A HIS* 3.0 45.0 + - + -
329A ILE* 3.8 16.4 - - + -
350A MET* 5.0 1.1 - - - -
451A LEU* 3.3 39.8 + - + +
453A ALA 3.2 1.0 - - - -
454A ILE* 1.3 78.0 - - + +
456A GLN* 1.3 66.5 + - - +
457A HIS 3.1 2.9 + - - -
458A PHE 3.5 6.3 - - - +
460A LEU* 3.9 36.6 - - + -
492A ARG* 3.5 2.9 + - - -
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Residues in contact with GLN 456 (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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155A LEU* 5.0 0.9 - - - +
329A ILE* 4.0 21.4 - - + +
330A ASP* 5.0 0.7 - - - +
333A ILE* 3.4 4.6 - - - +
334A GLY 3.3 25.6 + - - +
335A PRO* 4.3 12.5 - - + +
336A SER 3.5 7.9 - - - +
337A ARG 2.6 31.7 + - - +
338A ILE* 4.4 2.8 - - - +
339A PRO* 3.4 22.1 - - + +
452A CYS 2.9 14.5 + - - +
453A ALA* 3.2 12.0 - - - +
455A LEU* 1.3 75.1 - - - +
457A HIS* 1.3 86.4 + - + +
492A ARG* 3.9 18.4 + - - +
493A SER* 5.5 0.7 + - - -
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Residues in contact with HIS 457 (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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155A LEU* 3.4 26.1 - - + +
159A ARG* 4.2 14.3 + - - +
335A PRO 4.0 17.2 + - - -
336A SER* 4.9 6.5 + - - -
453A ALA 3.3 11.4 - - - -
454A ILE 3.2 3.0 + - - +
455A LEU 3.1 0.6 - - - -
456A GLN* 1.3 109.3 + - + +
458A PHE* 1.3 86.1 + - + +
491A PRO* 3.3 4.3 - - - +
492A ARG* 2.9 29.2 + - - +
493A SER* 3.8 18.7 + - - +
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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
------------------------------------------------------------
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