Contacts of the helix formed by residues 442 - 460 (chain B) in PDB entry 3EHN
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 SER 442 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B LEU* 1.3 71.6 - - - +
443B LYS* 1.3 57.3 + - - +
444B GLN* 2.9 8.1 - - - +
445B GLU* 2.7 53.6 + - - +
446B GLU 2.8 9.4 + - - -
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Residues in contact with LYS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B TYR* 3.2 54.6 - - + +
441B LEU 3.4 3.9 + - - -
442B SER* 1.3 70.2 - - - +
444B GLN* 1.3 56.4 - - - +
446B GLU* 3.9 1.1 - - - -
447B GLN* 2.8 46.9 + - - +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.5 32.1 + - + +
371B TYR* 3.3 40.3 + - + +
442B SER* 2.7 10.9 + - - +
443B LYS* 1.3 74.1 - - - +
445B GLU* 1.3 67.6 + - + +
447B GLN* 2.9 21.6 + - - +
448B LEU* 2.9 12.7 + - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B TYR* 3.2 23.2 + - - -
441B LEU* 3.8 19.7 - - + +
442B SER* 2.7 31.6 + - - +
444B GLN* 1.3 75.9 - - + +
446B GLU* 1.3 55.9 + - - +
448B LEU* 3.1 7.5 + - - +
449B GLN* 2.9 23.5 + - - -
475B PHE* 3.5 9.9 - - - -
537B ARG* 2.8 36.3 + - - -
541B PRO* 3.0 17.5 - - - +
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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
----------------------------------------------------------
430B THR* 2.9 32.5 + - - +
436B ASP 3.2 1.9 - - - +
437B TYR* 2.9 37.2 - - + +
438B THR* 2.7 30.5 + - - -
439B GLY* 3.4 9.0 + - - -
441B LEU* 4.2 16.6 + - + +
442B SER 2.8 12.5 + - - +
443B LYS 4.1 3.4 - - - +
445B GLU* 1.3 72.0 - - - +
447B GLN* 1.3 58.2 + - - +
448B LEU 3.0 5.2 - - - -
449B GLN* 3.6 10.9 - - - +
450B LYS* 2.8 41.5 + - - +
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.5 17.9 - - + +
434B TRP* 3.0 45.2 - - + +
437B TYR* 2.7 32.4 + - + +
443B LYS* 2.8 38.1 + - - +
444B GLN* 2.9 13.3 + - - +
446B GLU* 1.3 77.5 - - - +
448B LEU* 1.3 57.6 + - - +
450B LYS* 4.4 2.2 - - - -
451B ILE* 3.0 29.1 + - - +
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Residues in contact with LEU 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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231B PHE* 3.9 9.9 - - + -
367B GLU* 3.3 40.2 - - + +
370B LEU* 4.8 2.0 - - + +
371B TYR* 3.6 21.5 - - + +
444B GLN 2.9 9.9 + - - +
445B GLU* 3.2 10.5 - - - +
447B GLN* 1.3 75.5 - - - +
449B GLN* 1.3 57.1 + - - +
450B LYS 3.0 1.6 - - - -
451B ILE* 2.7 31.0 + - + +
452B ILE* 2.8 28.1 + - + +
473B THR* 4.6 5.2 - - - -
475B PHE* 4.4 3.4 - - + -
537B ARG* 2.9 39.7 - - - +
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Residues in contact with GLN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLY 3.8 6.1 + - - +
429B ASN* 4.5 2.6 + - - -
430B THR* 3.0 38.9 + - + +
438B THR* 5.4 0.7 + - - -
441B LEU* 3.7 12.4 - - - +
445B GLU 2.9 12.0 + - - +
446B GLU* 3.6 11.3 - - - +
448B LEU* 1.3 74.6 - - - +
450B LYS* 1.3 59.8 + - - +
453B THR* 2.7 39.9 + - - +
475B PHE* 3.2 46.3 - - + -
476B PRO* 5.5 0.7 - - + -
477B TYR* 3.4 37.0 - - - +
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Residues in contact with LYS 450 (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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382B TYR* 3.1 24.3 - - - +
430B THR* 2.4 45.3 + - + -
431B SER 3.3 10.8 + - - +
433B LYS 2.8 28.5 + - - +
434B TRP* 3.9 35.0 - - + +
436B ASP 2.9 15.0 + - - -
437B TYR* 4.2 8.5 - - + -
446B GLU* 2.8 37.8 + - - +
447B GLN* 3.9 7.9 - - - +
449B GLN* 1.3 77.2 - - - +
451B ILE* 1.3 59.0 + - - +
453B THR* 4.0 2.1 - - - -
454B GLN* 3.2 20.3 + - - +
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Residues in contact with ILE 451 (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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363B PHE* 3.5 40.6 - - + +
366B ALA* 3.8 31.6 - - + +
367B GLU* 4.1 10.1 - - + +
370B LEU* 3.9 13.9 - - + -
378B PRO* 5.6 0.2 - - + -
382B TYR* 3.7 24.9 - - + -
434B TRP* 3.9 5.8 - - + -
447B GLN 3.0 20.9 - - - +
448B LEU* 2.7 18.5 + - + +
450B LYS* 1.3 67.9 - - - +
452B ILE* 1.3 62.0 - - + +
453B THR 3.1 1.3 + - - -
454B GLN* 3.4 1.7 + - - +
455B LYS* 2.8 32.4 + - + +
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Residues in contact with ILE 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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367B GLU* 3.4 25.8 - - + +
448B LEU* 2.8 29.0 + - + +
451B ILE* 1.3 74.9 - - + +
453B THR* 1.3 57.1 + - - +
455B LYS* 3.3 13.9 - - + +
456B TYR* 2.9 26.7 + - - +
469B GLU* 4.0 20.4 - - + +
472B ARG* 3.9 4.5 - - - +
473B THR* 3.3 33.0 - - + +
475B PHE* 3.0 40.8 - - + +
476B PRO* 3.8 1.8 - - + -
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Residues in contact with THR 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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293B TYR* 3.9 30.4 - - + -
297B TYR* 4.2 7.0 - - - +
429B ASN* 5.6 0.7 + - - -
430B THR* 5.4 2.8 - - - +
449B GLN* 2.7 29.7 + - - +
450B LYS* 4.0 3.8 - - - -
452B ILE* 1.3 73.2 - - - +
454B GLN* 1.3 64.6 + - - +
455B LYS 2.9 3.6 - - - -
456B TYR* 2.7 26.8 + - + +
457B LEU* 2.8 25.5 - - + +
476B PRO* 3.2 29.1 - - + +
477B TYR 4.9 0.2 + - - -
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Residues in contact with GLN 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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297B TYR* 3.3 25.5 - - - -
301B ARG* 3.7 12.6 + - - -
363B PHE* 3.6 13.0 - - + -
382B TYR* 3.1 36.7 + - + +
386B ILE* 3.9 16.4 - - + +
401B TYR* 2.7 44.5 + - - -
431B SER 5.5 0.8 + - - -
432B PRO* 4.7 4.8 - - - +
450B LYS 3.2 11.1 + - - +
451B ILE 4.1 0.9 - - - +
453B THR* 1.3 80.9 - - - +
455B LYS* 1.3 60.0 + - - +
457B LEU* 3.3 18.4 + - - +
458B ALA* 3.2 17.2 + - - +
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Residues in contact with LYS 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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224B ARG* 5.0 1.6 - - - +
360B GLU* 3.6 34.3 + - + -
363B PHE* 3.4 35.6 - - + +
364B LEU* 4.0 19.9 - - - +
367B GLU* 5.5 0.8 + - - -
451B ILE* 2.8 19.6 + - + +
452B ILE* 3.3 15.3 - - + +
453B THR 2.9 0.2 + - - -
454B GLN* 1.3 73.8 - - - +
456B TYR* 1.3 55.1 + - - +
458B ALA* 3.1 2.3 + - - +
459B LEU* 2.7 58.6 + - + +
465B GLU* 4.3 1.0 + - - -
469B GLU* 2.5 46.9 + - + +
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Residues in contact with TYR 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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78B ILE* 2.9 38.9 + - + -
79B GLY 3.6 6.1 + - - -
80B TYR* 2.6 56.5 + + - -
289B THR* 3.1 18.6 - - + +
290B ILE* 3.3 27.4 + - + +
293B TYR* 4.5 5.8 - + - -
452B ILE 2.9 13.1 + - - +
453B THR 2.7 10.9 + - - +
455B LYS* 1.3 76.6 - - - +
457B LEU* 1.3 78.9 + - + +
459B LEU* 3.5 8.0 + - - +
460B TYR 3.6 0.2 + - - -
466B ALA* 4.0 13.5 - - + -
476B PRO* 3.5 35.0 - - + -
478B LEU* 4.8 0.2 - - + -
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Residues in contact with LEU 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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80B TYR* 5.5 0.2 - - - -
290B ILE* 4.5 13.0 - - + -
293B TYR* 4.1 17.7 - - + -
294B LEU* 4.8 11.0 - - + +
297B TYR* 4.9 3.4 - - + -
299B ASP* 4.5 4.9 - - - +
301B ARG* 3.6 28.0 + - - +
305B TYR* 2.9 33.6 + - + -
401B TYR* 5.0 0.2 - - - +
453B THR* 2.8 42.8 + - + +
454B GLN* 3.3 31.9 - - - +
455B LYS 3.2 0.2 - - - -
456B TYR* 1.3 99.7 - - + +
458B ALA* 1.3 58.0 + - - +
460B TYR* 3.8 2.8 - - - +
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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
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301B ARG* 4.2 0.2 - - - +
305B TYR* 3.9 4.5 + - - -
357B ARG* 4.9 7.8 + - - -
359B SER* 3.8 17.3 + - - +
360B GLU* 5.4 1.1 - - + +
363B PHE* 3.7 30.3 - - + -
389B SER* 3.1 30.3 - - - +
392B GLU* 5.5 0.2 - - - +
393B GLN* 4.6 4.5 + - - -
454B GLN 3.2 3.0 + - - +
455B LYS 3.1 2.5 + - - +
457B LEU* 1.3 75.7 - - - +
459B LEU* 1.3 63.2 + - - +
460B TYR 3.0 14.9 + - - +
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Residues in contact with LEU 459 (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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80B TYR* 3.2 15.9 - - - +
357B ARG* 6.4 0.4 - - - -
360B GLU* 4.0 25.1 - - + +
455B LYS* 2.7 48.2 + - + +
456B TYR* 3.8 1.8 - - - +
457B LEU 3.5 0.2 - - - -
458B ALA* 1.3 73.5 - - - +
460B TYR* 1.3 51.3 + - - +
462B ASN* 2.5 45.4 + - + +
465B GLU* 3.6 39.7 - - + +
466B ALA* 4.1 16.6 - - + +
469B GLU* 4.6 4.0 - - + -
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Residues in contact with TYR 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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80B TYR* 3.2 36.9 + + + -
81B PHE* 3.4 26.9 - + - -
274B MET* 4.7 1.7 - - - +
290B ILE* 3.8 8.5 - - + -
305B TYR* 3.3 62.4 + + + -
306B PHE* 3.4 19.3 - + - -
345B PRO* 3.1 32.1 - - - +
354B TYR* 5.4 0.3 - - - -
357B ARG* 4.5 11.1 + - - -
393B GLN* 4.7 0.3 + - - -
456B TYR 3.6 0.8 + - - -
457B LEU 3.8 3.6 - - - +
458B ALA 3.0 9.3 + - - +
459B LEU* 1.3 78.0 - - - +
461B PRO* 1.3 84.2 - - + +
462B ASN 3.6 0.9 - - - +
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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
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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