Contacts of the helix formed by residues 587 - 596 (chain C) in PDB entry 4KPE
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 ASN 587 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B MET 4.0 10.7 + - - -
102B HIS* 3.9 23.1 + - - -
103B GLY* 2.8 35.0 + - - +
585C GLU 4.1 0.4 + - - -
586C MET* 1.3 74.1 - - - +
588C ALA* 1.3 53.8 + - - +
589C ASP* 2.6 5.5 + - + +
590C GLN* 2.4 57.4 + - - +
591C LEU* 3.2 6.0 + - - -
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Residues in contact with ALA 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 3.9 9.0 - - + -
440C SER* 4.2 8.2 + - - +
443C GLN* 3.8 19.5 - - + +
444C GLY* 3.4 33.9 - - - +
586C MET 4.1 1.8 + - - -
587C ASN* 1.3 68.6 - - - +
589C ASP* 1.3 64.2 + - - +
591C LEU* 3.9 7.8 - - - +
592C TRP* 3.1 25.5 + - - +
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Residues in contact with ASP 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 4.6 14.8 - - + +
587C ASN* 2.6 9.0 + - + +
588C ALA* 1.3 78.2 - - - +
590C GLN* 1.3 64.3 + - + +
592C TRP* 3.7 3.5 - - - +
593C GLU* 3.3 21.7 + - - +
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Residues in contact with GLN 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B HIS* 4.9 14.4 - - - -
557C TYR* 3.0 31.2 + - + +
580C TYR* 3.7 17.1 + - - -
585C GLU 4.6 1.6 - - - +
586C MET* 3.7 15.2 - - + +
587C ASN* 2.4 47.7 + - - +
589C ASP* 1.3 72.5 - - + +
591C LEU* 1.3 54.1 + - - +
593C GLU* 3.3 4.0 + - - -
594C THR* 2.6 41.7 + - - +
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Residues in contact with LEU 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ALA 5.2 0.9 - - - +
440C SER* 3.9 35.7 - - - +
441C ALA* 4.3 7.6 - - - +
444C GLY* 5.3 0.9 - - - -
504C MET* 4.3 15.3 - - + -
583C LEU* 5.3 17.9 - - + +
586C MET* 4.0 20.3 - - + +
587C ASN 3.2 5.0 + - - +
588C ALA* 4.1 12.8 - - - +
589C ASP 3.5 0.2 - - - -
590C GLN* 1.3 77.9 - - - +
592C TRP* 1.3 58.3 + - - +
594C THR* 3.5 5.8 - - - -
595C THR* 2.9 36.1 + - + +
596C MET* 3.0 31.0 + - + -
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Residues in contact with TRP 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 2.9 36.5 - - - +
444C GLY* 3.4 23.2 + - - +
445C ARG 4.0 0.9 - - - -
446C ASP* 3.6 27.6 - - + -
449C PHE* 4.9 1.6 - + - -
450C GLN* 3.4 23.8 - - - -
588C ALA 3.1 19.5 + - - +
589C ASP 3.7 2.0 - - - +
591C LEU* 1.3 79.5 - - - +
593C GLU* 1.3 71.1 + - + +
596C MET* 3.2 24.8 + - + +
597C ASN* 2.7 57.8 + - + +
598C PRO* 3.7 17.0 - - + -
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Residues in contact with GLU 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C TYR* 5.7 4.5 - - + -
589C ASP 3.3 13.5 + - - +
590C GLN* 4.0 3.6 - - - +
592C TRP* 1.3 87.9 - - + +
594C THR* 1.3 64.3 + - + +
597C ASN* 4.0 6.8 - - - +
600C THR* 2.9 31.3 - - - +
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Residues in contact with THR 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C LEU 4.7 1.0 - - - +
541C PRO* 3.9 12.8 - - + -
557C TYR* 3.6 51.6 - - + -
559C TRP* 3.8 22.0 - - + -
586C MET* 3.9 4.2 - - - -
590C GLN* 2.6 30.7 + - + +
591C LEU* 3.4 2.9 + - - -
593C GLU* 1.3 79.2 - - + +
595C THR* 1.3 82.5 + - - +
600C THR 4.0 3.0 - - - +
601C ARG* 3.9 13.1 - - - -
602C THR 4.6 1.4 + - - -
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Residues in contact with THR 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C TYR* 4.1 6.1 + - - -
504C MET* 4.0 14.0 - - - +
538C ALA* 4.5 9.7 - - - +
539C LEU 4.0 15.5 - - - -
540C PRO* 3.7 10.6 - - + +
541C PRO* 3.4 23.8 - - + -
583C LEU* 5.9 0.8 - - + +
586C MET* 4.6 3.1 - - - -
591C LEU* 2.9 26.4 + - + +
592C TRP 3.6 0.2 + - - -
594C THR* 1.3 92.9 - - - +
596C MET* 1.3 61.5 + - - +
601C ARG* 3.5 23.5 - - - +
602C THR 5.0 2.9 - - - +
603C LEU* 5.0 1.0 - - - +
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Residues in contact with MET 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C TYR* 3.7 43.5 - - + +
441C ALA* 4.2 30.7 - - + +
444C GLY 4.5 3.6 - - - -
445C ARG* 3.9 30.1 - - + -
450C GLN* 3.3 9.1 + - - +
452C ILE* 4.4 1.8 - - + -
504C MET* 4.3 6.5 - - - +
591C LEU* 3.0 36.5 + - + +
592C TRP* 3.7 15.7 - - + -
595C THR* 1.3 81.9 - - - +
597C ASN* 1.3 66.1 + - - +
598C PRO* 3.1 10.9 - - - +
601C ARG* 3.1 13.0 + - - -
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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