Contacts of the helix formed by residues 444 - 451 (chain B) in PDB entry 1KPS
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 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439B PHE* 3.2 11.0 - - - -
442B PHE 3.4 0.6 + - - -
443B PRO* 1.3 74.6 - - - +
445B PRO* 1.3 70.6 - - - +
446B GLU* 3.3 17.0 + - - +
447B LYS* 3.5 35.0 + - - +
448B LEU* 3.0 24.4 + - - +
481B VAL* 3.1 9.5 - - - +
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Residues in contact with PRO 445 (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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444B SER* 1.3 90.6 - - - +
446B GLU* 1.3 59.5 + - - +
448B LEU* 3.6 2.9 - - - +
449B LEU* 3.3 29.7 + - - +
481B VAL* 3.2 22.0 - - + +
483B ARG* 3.2 51.1 - - - +
488B VAL* 4.1 17.8 - - + +
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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
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444B SER* 3.1 10.1 + - - +
445B PRO* 1.3 76.8 - - + +
447B LYS* 1.3 70.5 + - - +
448B LEU 3.0 2.3 + - - -
449B LEU* 3.0 19.4 + - - +
450B ARG* 2.8 55.2 + - + +
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Residues in contact with LYS 447 (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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438B THR* 3.7 30.1 - - - +
439B PHE* 3.8 20.4 - - + -
442B PHE* 3.0 36.5 + - - +
443B PRO 4.7 0.2 + - - -
444B SER* 3.5 17.8 + - - +
446B GLU* 1.3 83.3 - - + +
448B LEU* 1.3 62.6 + - - +
450B ARG* 3.4 23.2 + - - +
451B LEU* 3.4 18.8 + - + +
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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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439B PHE* 3.6 31.4 - - + -
444B SER 3.0 18.1 + - - +
445B PRO 3.6 5.4 - - - +
446B GLU 3.0 0.2 - - - -
447B LYS* 1.3 75.5 - - - +
449B LEU* 1.3 66.8 + - + +
451B LEU* 3.1 21.5 + - + +
455B VAL* 3.9 30.9 - - + +
459B ILE* 5.5 0.4 - - + -
478B VAL* 4.8 12.3 - - + -
481B VAL* 3.9 6.3 - - + -
488B VAL* 4.6 5.2 - - + +
491B ALA* 3.5 32.5 - - + -
492B VAL* 3.6 25.8 - - + +
495B ALA* 5.5 2.2 - - + -
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Residues in contact with LEU 449 (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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445B PRO 3.3 13.9 + - - +
446B GLU* 3.0 11.2 + - - +
448B LEU* 1.3 79.0 - - + +
450B ARG* 1.3 62.4 + - + +
452B GLY* 3.3 14.9 + - - -
455B VAL* 5.4 0.6 - - - +
487B SER* 4.3 33.4 - - - +
488B VAL* 4.2 17.7 - - + +
491B ALA* 4.3 15.5 - - + -
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Residues in contact with ARG 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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435B ASP* 5.3 8.9 - - - +
446B GLU* 2.8 56.8 + - + +
447B LYS* 3.5 16.5 - - - +
448B LEU 3.1 0.2 - - - -
449B LEU* 1.3 73.4 - - + +
451B LEU* 1.3 63.1 + - - +
452B GLY* 2.8 9.3 + - - -
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Residues in contact with LEU 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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435B ASP* 4.1 35.7 - - + +
436B LEU* 3.2 39.3 - - + +
439B PHE* 4.4 13.7 - - + -
447B LYS* 3.5 17.0 - - + +
448B LEU* 3.1 11.3 + - - +
450B ARG* 1.3 76.9 - - - +
452B GLY* 1.3 59.4 + - - +
454B LYS* 4.5 13.9 - - - +
455B VAL* 3.4 32.2 + - + +
458B LEU* 4.7 15.8 - - + +
459B ILE* 4.4 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