Contacts of the helix formed by residues 424 - 429 (chain B) in PDB entry 3KSA
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 LEU 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A LEU* 6.2 1.8 - - + -
389A ILE* 5.1 13.2 - - + -
392A ILE* 4.1 20.9 - - + +
419A ILE* 3.4 24.7 - - + +
420A VAL* 3.0 17.8 + - - +
422A LEU* 3.1 26.2 + - + +
423A GLN 4.3 4.9 - - - +
424A LEU* 3.9 24.2 - - + -
427A LEU* 4.8 16.8 - - + -
423B GLN* 1.3 75.2 - - - +
425B TYR* 1.3 57.4 + - - +
426B ARG 2.8 5.4 - - - -
427B LEU* 2.8 43.9 + - + +
428B THR 4.0 0.3 + - - -
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Residues in contact with TYR 425 (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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392A ILE* 4.4 6.9 - - - +
398A LYS* 3.4 36.6 - - + +
401A ALA* 5.0 1.8 - - + -
420A VAL* 3.2 38.8 + - + +
421A THR* 4.5 9.9 - - + -
423B GLN* 2.9 37.7 + - + -
424B LEU* 1.3 78.3 - - - +
426B ARG* 1.3 86.2 + - - +
427B LEU 3.1 0.4 - - - -
428B THR* 2.8 37.2 + - + +
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Residues in contact with ARG 426 (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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371B ARG* 6.0 2.6 - - - +
378B LEU* 6.1 1.6 - - - +
422B LEU* 4.3 29.2 - - + +
423B GLN* 3.7 32.1 + - + +
424B LEU 2.8 0.8 - - - -
425B TYR* 1.3 110.5 + - + +
427B LEU* 1.3 59.5 + - + +
429B ASN* 3.1 32.5 + - - +
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Residues in contact with LEU 427 (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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389A ILE* 4.4 6.5 - - + -
392A ILE* 4.8 5.6 - - + -
393A ARG* 3.6 42.9 - - + +
424A LEU* 4.8 17.5 - - + -
385B LEU* 3.9 27.1 - - + +
389B ILE* 3.6 21.3 - - + -
422B LEU* 5.4 6.7 - - + -
423B GLN 4.9 3.1 - - - +
424B LEU* 2.8 36.3 + - + +
426B ARG* 1.3 75.4 - - + +
428B THR* 1.3 61.4 + - - +
429B ASN 3.0 7.8 + - - -
430B THR* 3.8 14.8 + - - +
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Residues in contact with THR 428 (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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392A ILE* 3.4 19.8 + - - +
393A ARG 4.7 2.5 - - - +
395A SER* 3.1 29.7 + - - +
396A GLU* 3.4 20.3 - - - +
397A ASN* 3.4 29.2 + - - -
398A LYS 3.8 3.1 - - - +
401A ALA* 4.0 2.6 - - - +
424B LEU 4.0 0.8 + - - -
425B TYR* 2.8 28.6 + - + +
427B LEU* 1.3 79.1 - - - +
429B ASN* 1.3 65.4 + - + +
430B THR 3.7 2.3 + - - -
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Residues in contact with ASN 429 (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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396A GLU 5.3 0.9 - - - +
425B TYR 5.1 0.2 - - - +
426B ARG* 3.1 22.8 + - - +
427B LEU* 3.0 1.5 - - - -
428B THR* 1.3 85.5 - - + +
430B THR* 1.3 57.8 + - - +
431B ASP* 3.6 21.7 + - - +
434B VAL* 4.2 16.4 - - - +
435B LEU* 5.7 6.8 - - - +
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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