Contacts of the helix formed by residues 394 - 402 (chain B) in PDB entry 1KTW
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 LYS 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B PHE* 4.1 16.2 - - + -
273B LEU* 4.4 22.2 - - + -
303B ARG* 4.8 10.3 - - - +
393B LEU* 1.3 81.0 - - - +
395B GLN* 1.3 65.5 + - - +
396B ASP* 2.9 23.3 - - - +
397B GLN* 3.0 39.8 + - - +
398B LEU* 3.8 9.2 - - - +
424B GLN* 3.1 31.7 + - - +
425B ILE* 5.4 0.2 - - + -
426B TYR* 4.2 2.5 - - - -
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Residues in contact with GLN 395 (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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394B LYS* 1.3 74.9 - - - +
396B ASP* 1.3 57.3 + - - +
397B GLN 3.1 4.1 + - - -
398B LEU* 3.6 17.6 + - + +
399B ASP 5.1 0.2 + - - -
423B GLY* 3.7 14.8 + - - +
426B TYR* 2.4 53.0 + - + +
478B TYR* 3.4 44.6 + - + +
479B TYR* 3.2 31.9 + - - -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LYS* 2.9 28.2 - - - +
395B GLN* 1.3 72.1 + - - +
397B GLN* 1.3 63.3 + - - +
398B LEU 3.6 0.4 - - - -
399B ASP* 5.1 4.6 + - - +
400B TYR* 4.1 12.5 - - - -
478B TYR* 5.4 1.6 - - - -
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 5.2 2.7 - - - +
299B GLY* 5.7 2.6 - - - -
303B ARG* 4.8 16.8 - - - +
392B ASP 4.8 1.0 - - - +
393B LEU* 3.8 10.2 - - + +
394B LYS* 3.0 38.7 + - - +
395B GLN 3.1 1.2 - - - -
396B ASP* 1.3 92.5 + - - +
398B LEU* 1.3 65.5 + - - +
399B ASP 3.2 4.0 + - - -
400B TYR* 3.3 24.8 + - + +
401B PHE* 5.1 0.2 - - - -
431B LEU* 3.4 37.7 - - + +
435B ILE* 4.0 24.7 - - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 4.2 16.2 - - + -
394B LYS 3.8 10.8 - - - +
395B GLN* 3.6 26.6 + - - +
397B GLN* 1.3 78.4 - - - +
399B ASP* 1.3 60.1 + - - +
400B TYR 3.2 1.3 - - - -
401B PHE* 2.9 44.7 - - + +
411B VAL* 4.8 7.4 - - + -
426B TYR* 4.1 34.3 - - + -
475B VAL* 4.2 2.4 - - - +
476B CYS* 3.9 26.7 - - + -
478B TYR* 4.1 23.8 - - + -
481B MET* 4.6 2.5 - - + -
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLN 5.7 0.2 - - - -
396B ASP* 5.1 4.5 - - - +
397B GLN* 3.2 1.8 - - - +
398B LEU* 1.3 75.9 - - - +
400B TYR* 1.3 59.0 + - + +
401B PHE 3.0 9.3 + - - -
402B SER* 3.3 17.1 + - - -
472B SER* 3.2 24.5 + - - +
473B SER* 3.6 17.5 + - - +
474B ARG* 2.9 42.8 + - - +
475B VAL* 4.0 2.1 + - - -
478B TYR* 3.3 22.0 + - - -
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Residues in contact with TYR 400 (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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396B ASP 4.1 15.0 - - - -
397B GLN* 3.6 27.4 - - + +
398B LEU 3.2 2.2 - - - -
399B ASP* 1.3 78.3 - - + +
401B PHE* 1.3 61.4 + - - +
402B SER* 3.3 2.2 - - - -
403B THR* 4.4 2.1 + - - -
404B SER* 4.8 3.3 + - - -
431B LEU* 4.1 11.2 - - + +
437B THR* 5.7 4.2 - - - +
463B HIS* 3.3 26.8 + - + -
466B ILE* 3.9 41.0 - - + +
467B ASP 4.6 5.7 + - - -
470B THR* 3.9 37.1 + - + -
472B SER* 3.7 27.7 + - - -
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Residues in contact with PHE 401 (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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393B LEU* 3.8 11.0 - - + -
398B LEU* 2.9 52.5 - - + +
399B ASP 3.0 0.6 - - - -
400B TYR* 1.3 78.2 - - - +
402B SER* 1.3 62.2 + - - +
403B THR 3.1 3.3 + - - -
404B SER* 4.0 7.2 - - - -
405B ASN* 2.6 67.5 + - + +
408B CYS* 4.8 0.9 - - - -
411B VAL* 4.6 5.8 - - + -
429B PRO* 3.7 43.1 - - + -
430B SER 4.3 3.6 - - - -
431B LEU* 3.6 27.6 - - + -
475B VAL* 4.2 5.8 - - + -
476B CYS* 3.9 13.0 - - - -
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Residues in contact with SER 402 (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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399B ASP 3.3 17.8 + - - -
400B TYR* 4.8 1.2 - - - -
401B PHE* 1.3 78.6 - - - +
403B THR* 1.3 70.6 + - - +
406B PRO* 3.8 17.5 - - - +
463B HIS* 5.4 0.3 + - - -
471B GLU* 4.3 1.2 + - - +
472B SER* 3.6 14.9 - - - -
473B SER* 3.5 28.7 - - - -
475B VAL* 4.2 15.5 - - - +
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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