Contacts of the helix formed by residues 437 - 445 (chain D) in PDB entry 3FAA
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 437 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376D LYS* 4.3 7.9 - - - +
435D ASP* 3.5 3.0 + - - -
436D PRO* 1.3 77.7 - - - +
438D VAL* 1.3 64.3 + - - +
439D GLU* 3.5 7.1 + - - +
440D GLU* 2.9 40.6 + - - +
441D MET* 3.4 19.9 + - - +
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Residues in contact with VAL 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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372D ARG* 3.8 48.0 - - - +
376D LYS* 3.3 37.5 - - + +
379D MET* 4.9 0.4 - - + -
384D LEU* 4.3 17.9 - - + +
437D SER* 1.3 70.6 - - - +
439D GLU* 1.3 68.9 + - - +
440D GLU 3.0 1.7 + - - -
441D MET* 3.2 5.0 + - - +
442D ARG* 2.9 27.9 + - + +
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Residues in contact with GLU 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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437D SER* 3.5 5.9 + - - +
438D VAL* 1.3 79.4 - - - +
440D GLU* 1.3 62.3 + - + +
442D ARG* 3.6 13.3 - - + +
443D LYS* 3.1 25.6 + - + +
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Residues in contact with GLU 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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432D VAL* 4.4 10.1 - - + -
433D PRO* 2.8 36.0 - - + +
435D ASP 4.5 1.2 - - - +
436D PRO* 3.5 8.8 - - - +
437D SER* 2.9 45.0 + - - +
438D VAL 3.0 0.8 - - - -
439D GLU* 1.3 75.0 - - + +
441D MET* 1.3 61.7 + - - +
443D LYS* 2.8 28.5 + - - +
444D VAL* 3.0 12.9 + - + +
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Residues in contact with MET 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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376D LYS* 3.3 20.6 - - + +
377D ARG* 3.8 27.8 - - - +
379D MET 5.5 1.1 - - - +
384D LEU* 3.7 23.1 - - + -
428D TYR* 4.3 16.6 - - + -
432D VAL* 3.6 27.6 - - + -
436D PRO* 3.9 11.0 - - + -
437D SER 3.4 13.2 + - - +
438D VAL 3.2 3.2 + - - +
440D GLU* 1.3 72.5 - - - +
442D ARG* 1.3 61.6 + - - +
443D LYS 2.8 2.5 + - - -
444D VAL* 3.0 4.8 + - + +
445D VAL* 2.6 60.1 + - + +
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Residues in contact with ARG 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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372D ARG* 5.2 4.8 - - - +
384D LEU* 3.8 29.7 + - + +
385D ASP* 3.5 39.8 + - + +
386D ASP* 5.4 1.8 - - - +
438D VAL* 2.9 21.0 + - - +
439D GLU* 3.6 15.7 - - + +
441D MET* 1.3 75.6 - - - +
443D LYS* 1.3 65.1 + - - +
446D CYS* 3.1 26.4 + - + +
447D GLU* 3.2 13.7 + - + +
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Residues in contact with LYS 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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439D GLU* 3.1 17.8 + - + +
440D GLU* 2.8 17.9 + - - +
441D MET 2.8 0.6 + - - -
442D ARG* 1.3 80.6 - - - +
444D VAL* 1.3 63.7 + - + +
445D VAL 3.2 0.3 + - - -
447D GLU* 3.2 34.9 + - + +
448D GLN* 3.2 31.8 + - - +
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Residues in contact with VAL 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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428D TYR* 4.1 14.4 - - + -
431D LEU* 3.3 64.6 - - + +
432D VAL* 4.3 13.2 - - + -
440D GLU* 3.0 14.3 + - + +
441D MET* 3.9 4.5 - - + +
443D LYS* 1.3 76.8 - - + +
445D VAL* 1.3 61.1 + - + +
448D GLN* 3.8 5.1 - - - +
449D LYS 3.7 2.6 + - - -
450D LEU* 3.1 36.0 + - + +
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Residues in contact with VAL 445 (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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379D MET 5.5 0.2 - - - +
381D PRO* 3.4 28.9 - - + -
384D LEU* 3.7 15.9 - - + -
402D TYR* 3.9 4.7 - - - +
428D TYR* 3.5 38.8 - - + +
441D MET* 2.6 34.5 + - + +
444D VAL* 1.3 72.5 - - - +
446D CYS* 1.3 61.8 + - - +
447D GLU 3.4 0.4 - - - -
449D LYS* 3.0 26.7 - - - +
450D LEU 3.9 2.0 - - - +
451D ARG* 3.1 23.3 + - - +
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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