Contacts of the helix formed by residues 436 - 445 (chain P) in PDB entry 5KZ5
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 MET 436 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364P GLU* 3.5 40.4 - - + +
432P ARG 3.2 6.9 + - - +
433P LEU* 3.2 21.9 + - + +
434P ARG 3.3 0.8 - - - +
435P GLU* 1.4 74.3 - - - +
437P SER* 1.3 62.6 + - - +
439P LEU* 3.4 0.9 + - - +
440P TRP* 3.3 79.5 + - + -
93i PHE* 3.8 20.0 - - + -
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Residues in contact with SER 437 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434P ARG 3.2 19.5 + - - +
435P GLU* 3.3 4.5 - - - -
436P MET* 1.3 81.6 - - - +
438P PRO* 1.3 60.8 - - - +
440P TRP* 4.9 2.2 - - - +
441P GLU* 3.3 25.8 + - - +
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Residues in contact with PRO 438 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435P GLU* 4.1 8.5 - - + +
437P SER* 1.3 85.1 - - - +
439P LEU* 1.4 61.9 + - - +
440P TRP 3.3 1.3 - - - -
441P GLU* 3.3 39.6 + - + +
442P MET* 3.5 12.5 + - - +
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Residues in contact with LEU 439 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I SER* 5.6 6.5 + - - +
432P ARG* 3.4 51.4 - - + +
435P GLU* 3.1 38.0 + - + +
436P MET 3.4 5.6 + - - +
438P PRO* 1.4 75.3 - - - +
440P TRP* 1.4 61.2 + - - +
441P GLU 3.7 0.2 + - - -
442P MET* 3.7 14.4 + - - +
443P VAL* 4.0 11.1 - - - +
72i VAL* 5.4 5.3 - - + +
91i LYS* 5.3 1.1 - - + -
93i PHE* 4.0 29.8 - - + -
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Residues in contact with TRP 440 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3864 LEU* 3.4 46.7 - - + +
3984 ASP* 5.3 8.3 - - - -
3994 GLU* 5.8 0.7 - - - -
364P GLU* 5.1 3.1 - - - -
436P MET* 3.3 49.2 + - + +
437P SER* 5.3 1.8 - - - -
439P LEU* 1.4 76.7 - - - +
441P GLU* 1.4 65.3 + - + +
442P MET 3.5 0.3 + - - -
443P VAL* 3.5 3.2 + - - -
444P GLN* 3.3 21.0 + - + +
71i ASP* 4.2 18.4 - - - -
72i VAL* 5.2 4.8 - - + +
93i PHE* 3.5 46.0 - + + -
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Residues in contact with GLU 441 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437P SER* 3.3 18.4 + - - +
438P PRO* 3.3 32.5 + - + +
440P TRP* 1.4 78.9 - - + +
442P MET* 1.4 61.5 + - - +
444P GLN* 3.0 30.9 - - + +
445P ASP* 3.0 22.9 + - - +
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Residues in contact with MET 442 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3131 GLN* 2.9 39.9 + - - +
52I PRO* 4.1 13.5 - - - +
55I ALA* 4.0 16.8 - - + +
56I SER* 3.9 37.0 - - - +
59I GLN* 5.4 6.5 - - + -
438P PRO 3.5 8.8 + - - +
439P LEU* 4.0 9.9 - - - +
440P TRP 3.3 1.0 - - - -
441P GLU* 1.4 78.5 - - - +
443P VAL* 1.4 64.6 + - - +
445P ASP* 3.5 12.5 + - - +
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Residues in contact with VAL 443 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3131 GLN* 3.6 9.5 - - - +
3854 SER* 4.5 5.2 + - - -
3864 LEU* 3.8 29.8 - - + +
52I PRO* 3.8 24.2 - - + +
53I ARG* 3.6 23.6 - - - +
56I SER* 5.8 2.5 - - - +
439P LEU 4.0 12.1 - - - +
440P TRP 3.5 5.8 + - - +
441P GLU 3.3 0.2 - - - -
442P MET* 1.4 85.4 - - - +
444P GLN* 1.4 60.2 + - - +
446P GLY 3.6 7.3 - - - +
449P LEU* 3.6 7.8 - - - +
72i VAL* 4.0 26.7 - - + -
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Residues in contact with GLN 444 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3864 LEU* 4.8 5.8 - - + -
3874 GLU* 3.1 51.2 + - + +
440P TRP* 3.3 18.4 + - + +
441P GLU* 3.0 28.6 + - + +
443P VAL* 1.4 79.7 - - - +
445P ASP* 1.4 76.8 + - - +
446P GLY 3.4 2.2 + - - -
447P ILE* 4.1 9.0 - - - +
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Residues in contact with ASP 445 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3131 GLN* 3.8 12.9 - - + +
441P GLU* 3.0 30.2 + - - +
442P MET* 3.5 14.1 - - - +
443P VAL 3.4 2.0 - - - -
444P GLN* 1.4 87.6 + - - +
446P GLY* 1.3 58.5 + - - +
447P ILE* 5.0 2.1 - - - +
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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