Contacts of the helix formed by residues 435 - 446 (chain D) in PDB entry 3ER8
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 TYR 435 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279D THR* 4.5 14.5 - - + +
320D HIS* 3.6 14.1 + + - -
425D LEU* 3.8 18.8 - - + +
428D GLN* 3.8 15.0 - - + -
429D MET* 3.9 37.7 - - + -
432D SER* 6.2 1.6 - - - -
433D GLY 3.1 25.4 + - - +
434D GLU* 1.3 76.6 + - - +
436D LYS* 1.3 120.7 + - + +
437D GLN 3.6 1.8 - - - -
438D CYS* 3.3 8.9 + - - +
439D LEU* 3.1 28.1 + - + +
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Residues in contact with LYS 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D HIS* 3.0 54.3 + - + +
322D ILE* 4.9 10.1 - - + +
434D GLU* 5.9 2.2 - - - +
435D TYR* 1.3 118.4 + - + +
437D GLN* 1.3 63.9 + - - +
439D LEU* 3.1 20.0 - - + +
440D SER* 3.3 5.8 + - - -
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Residues in contact with GLN 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D VAL* 5.8 1.2 - - - +
328D ARG* 4.6 9.7 - - - +
351D TYR* 5.0 6.1 - - + -
435D TYR 3.6 0.4 - - - -
436D LYS* 1.3 77.2 - - - +
438D CYS* 1.3 71.6 + - - +
440D SER* 2.9 35.6 + - - -
441D ASP* 2.6 43.7 + - - +
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Residues in contact with CYS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D MET* 3.0 22.5 - - + +
333D MET* 6.2 0.9 - - + -
351D TYR* 3.3 32.5 - - + -
352D PHE* 3.9 27.1 - - + -
421D CYS* 5.9 1.3 - - - -
425D LEU* 3.6 20.2 - - + -
434D GLU* 4.4 2.2 - - - -
435D TYR* 3.8 12.8 - - - -
437D GLN* 1.3 75.4 - - - +
439D LEU* 1.3 64.9 + - - +
441D ASP 3.1 0.7 + - - -
442D LEU* 2.7 22.3 + - - +
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Residues in contact with LEU 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D THR* 3.7 31.6 - - + +
282D LEU* 5.8 4.3 - - + -
283D LEU* 3.6 34.8 - - + +
286D ILE* 6.1 0.9 - - + -
316D VAL* 3.7 19.7 - - + -
320D HIS* 6.4 0.4 - - + -
322D ILE* 4.9 4.7 - - + -
425D LEU* 4.0 6.2 - - + +
429D MET* 5.7 1.3 - - + -
435D TYR* 3.1 19.2 + - + +
436D LYS* 3.1 12.8 - - + +
438D CYS* 1.3 77.0 - - - +
440D SER* 1.3 55.5 + - - +
442D LEU* 2.6 33.3 + - + +
443D LEU* 2.7 35.3 + - + +
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Residues in contact with SER 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ILE* 4.3 18.8 - - - +
323D VAL* 3.8 22.6 + - - +
328D ARG* 4.2 2.3 - - - +
436D LYS 3.3 4.7 + - - -
437D GLN* 2.9 32.4 + - - -
439D LEU* 1.3 76.5 - - - +
441D ASP* 1.3 64.9 + - - -
443D LEU* 2.9 22.0 + - - +
444D ASN* 3.0 23.0 + - - -
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Residues in contact with ASP 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D ARG* 3.6 30.1 + - - +
329D ASN 3.0 18.2 - - - +
330D ASN* 4.6 2.4 - - - +
331D MET* 3.0 31.7 - - + +
351D TYR* 3.6 14.4 + - - -
437D GLN* 2.6 53.6 + - - +
440D SER* 1.3 72.6 + - - +
442D LEU* 1.3 53.3 + - - +
444D ASN* 3.7 0.3 + - - +
445D SER* 2.5 33.8 + - - -
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Residues in contact with LEU 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LEU* 4.7 1.8 - - + -
286D ILE* 3.7 31.9 - - + -
331D MET* 3.1 12.5 - - + +
418D ARG* 3.7 16.4 - - - +
421D CYS* 3.9 19.5 - - + -
422D ALA* 3.8 27.6 - - - +
425D LEU* 4.0 13.5 - - + -
438D CYS 2.7 12.2 + - - +
439D LEU* 2.6 30.3 + - + +
441D ASP* 1.3 69.9 - - - +
443D LEU* 1.3 64.7 + - + +
445D SER* 3.4 8.8 + - - -
446D MET* 3.0 28.4 - - + +
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Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D MET* 2.7 27.7 - - + +
282D LEU* 4.5 14.1 - - + -
286D ILE* 5.8 1.3 - - + -
313D LEU* 3.5 27.6 - - + -
316D VAL* 4.2 8.3 - - + -
322D ILE* 3.4 31.9 - - + -
324D PHE* 3.7 16.2 - - + -
439D LEU* 2.7 43.6 + - + +
440D SER* 3.4 4.9 - - - +
442D LEU* 1.3 74.3 - - + +
444D ASN* 1.3 66.8 + - - +
446D MET* 2.9 29.0 + - + +
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Residues in contact with ASN 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ILE* 5.3 0.4 - - - +
323D VAL* 3.2 27.1 + - - +
324D PHE* 3.7 3.8 - - - +
325D ASP* 3.4 22.4 - - - +
326D GLY 4.3 8.4 - - - +
328D ARG* 3.0 45.8 - - + +
440D SER* 3.0 14.7 + - - +
441D ASP 4.1 0.4 - - - +
443D LEU* 1.3 80.1 - - - +
445D SER* 1.3 61.1 + - - +
446D MET 2.9 1.7 + - - -
447D MET* 3.0 44.6 + - - +
449D ARG* 5.0 0.3 - - - -
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Residues in contact with SER 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ARG 4.0 7.1 + - - -
331D MET* 2.9 20.6 - - - +
332D PRO* 3.5 20.3 - - - +
414D GLU* 3.5 0.2 - - - +
418D ARG* 3.0 19.2 + - - -
441D ASP 2.5 25.1 + - - -
442D LEU 3.4 8.7 - - - -
443D LEU 3.1 0.4 + - - -
444D ASN* 1.3 75.7 - - - +
446D MET* 1.3 56.2 + - - +
447D MET 3.4 0.2 - - - -
449D ARG* 2.9 32.6 + - - +
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Residues in contact with MET 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D MET* 3.4 43.8 - - + +
144D SER* 3.2 22.4 + - - -
145D MET* 5.9 10.3 - - + +
282D LEU* 6.1 1.3 - - + -
286D ILE* 4.1 18.2 - - + -
313D LEU* 4.8 1.1 - - + -
418D ARG* 2.9 42.4 - - - +
442D LEU* 3.0 21.8 - - + +
443D LEU* 2.9 47.9 + - + +
445D SER* 1.3 74.9 - - - +
447D MET* 1.3 56.7 + - - +
449D ARG* 3.9 3.6 - - - -
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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