Contacts of the helix formed by residues 434 - 443 (chain D) in PDB entry 3MY0
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 434 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373D LYS* 3.8 3.1 - - - +
432D ASP 3.6 2.1 + - - -
433D PRO* 1.3 77.5 - - - +
435D PHE* 1.3 76.7 + - - +
436D GLU* 2.7 24.4 + - - +
437D ASP* 3.0 26.5 + - - -
438D MET* 3.2 24.6 + - - +
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Residues in contact with PHE 435 (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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373D LYS* 3.5 23.9 - - - +
376D MET* 3.9 34.1 - - + -
380D VAL* 4.2 9.0 - - + -
381D LEU* 3.8 40.8 - - + +
383D GLU* 4.7 18.8 - - + -
434D SER* 1.3 77.1 + - - +
436D GLU* 1.3 76.5 + - + +
438D MET* 3.7 0.4 + - - -
439D LYS* 3.1 31.4 + - + +
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Residues in contact with GLU 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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434D SER* 2.7 18.4 + - - +
435D PHE* 1.3 92.8 - - + +
437D ASP* 1.3 64.6 + - - +
438D MET 3.2 1.6 - - - -
439D LYS* 3.6 26.1 - - - +
440D LYS* 3.1 24.9 + - - +
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Residues in contact with ASP 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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429D VAL* 4.6 5.2 - - + -
430D PRO* 3.6 29.0 - - + +
433D PRO* 4.5 7.2 - - + -
434D SER* 3.0 35.5 + - - +
436D GLU* 1.3 79.3 - - - +
438D MET* 1.3 62.2 + - - +
440D LYS* 3.6 6.9 + - - +
441D VAL* 3.3 28.3 + - - +
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Residues in contact with MET 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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373D LYS* 3.6 21.1 - - + +
374D ARG* 3.5 32.5 - - - +
376D MET 5.2 1.6 - - - +
381D LEU* 3.7 22.9 - - + -
425D PHE* 4.0 14.1 - - + -
429D VAL* 3.9 25.6 - - + -
433D PRO* 4.1 14.4 - - + -
434D SER 3.2 15.5 + - - +
437D ASP* 1.3 73.8 - - - +
439D LYS* 1.3 60.6 + - - +
441D VAL* 3.2 1.7 + - + -
442D VAL* 2.7 64.0 + - + +
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Residues in contact with LYS 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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381D LEU* 3.5 39.1 + - + +
382D ASP* 4.4 16.6 + - - +
383D GLU* 5.7 3.0 + - - -
435D PHE* 3.1 24.3 + - + +
436D GLU* 3.6 32.8 - - - +
438D MET* 1.3 75.1 - - - +
440D LYS* 1.3 57.9 + - - +
443D CYS* 2.9 40.4 + - + +
444D VAL* 3.2 2.5 + - - +
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Residues in contact with LYS 440 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A ASN* 5.8 5.6 - - - +
457A ALA* 4.3 20.7 - - - +
436D GLU 3.1 17.0 + - - +
437D ASP* 3.8 7.0 - - - +
439D LYS* 1.3 78.3 - - - +
441D VAL* 1.3 59.0 + - + +
444D VAL* 3.3 12.9 + - + +
445D ASP* 2.8 58.3 + - - +
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Residues in contact with VAL 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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425D PHE* 3.8 31.0 - - + -
428D VAL* 3.8 19.7 - - + +
429D VAL* 3.6 22.0 - - + -
437D ASP 3.3 16.3 + - - +
438D MET* 3.2 4.8 + - + +
440D LYS* 1.3 84.2 - - + +
442D VAL* 1.3 62.0 + - + +
445D ASP* 3.5 9.1 - - - +
446D GLN 3.4 3.6 + - - -
447D GLN* 3.0 48.3 + - + +
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Residues in contact with VAL 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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376D MET 4.8 1.8 - - - +
378D PRO* 3.7 32.5 - - + +
381D LEU* 3.6 19.3 - - + -
399D TRP* 3.9 16.6 - - + -
425D PHE* 3.9 22.2 - - + -
438D MET* 2.7 47.8 + - + +
441D VAL* 1.3 73.1 - - + +
443D CYS* 1.3 57.6 + - - +
446D GLN* 3.3 22.8 - - - +
447D GLN 4.1 7.2 + - - +
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Residues in contact with CYS 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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378D PRO* 3.6 34.5 - - - -
381D LEU* 3.8 22.4 - - - -
382D ASP* 4.1 24.0 - - - +
439D LYS* 2.9 20.0 + - + +
442D VAL* 1.3 80.4 - - - +
444D VAL* 1.3 63.2 + - - +
445D ASP 3.5 0.2 - - - -
446D GLN* 3.1 19.6 - - - +
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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