Contacts of the helix formed by residues 441 - 452 (chain B) in PDB entry 1KHU
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 HIS 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A PRO* 3.6 42.1 - - + +
313A LEU* 5.7 1.4 - - - +
269B LYS 4.2 3.6 + - - +
270B HIS* 3.5 44.6 + + + +
271B TRP 3.3 5.6 + - - +
272B CYS* 3.8 4.0 - - - -
273B SER* 3.3 31.2 + - - -
288B HIS* 4.5 9.9 - + - -
439B HIS* 3.1 19.6 + - + +
440B LEU* 1.3 69.2 - - - +
442B GLY* 1.3 66.4 + - - +
444B LEU* 3.8 4.6 - - + +
445B GLN* 2.9 28.5 + - - +
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Residues in contact with GLY 442 (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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271B TRP* 4.4 6.5 + - - +
338B TYR* 5.6 4.3 - - - -
441B HIS* 1.3 79.9 - - - +
443B PRO* 1.3 70.9 - - - +
445B GLN* 3.1 6.0 + - - +
446B TRP* 3.1 44.1 + - - -
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Residues in contact with PRO 443 (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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271B TRP 5.6 0.2 - - - +
338B TYR* 5.9 3.1 - - + +
383B PHE* 3.3 35.9 - - + -
385B ASN* 3.8 2.0 - - - +
388B PHE* 3.7 14.7 - - + -
410B CYS* 3.6 20.4 - - + -
440B LEU* 3.3 22.2 - - + +
442B GLY* 1.3 89.1 - - - +
444B LEU* 1.3 62.0 + - - +
446B TRP* 3.3 23.5 + - + +
447B LEU* 2.9 25.1 + - - +
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Residues in contact with LEU 444 (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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300A THR* 3.0 30.0 + - - +
302A PRO* 4.2 4.0 - - + -
313A LEU* 4.0 31.6 - - + -
407B THR* 4.4 13.5 - - + -
410B CYS* 3.2 31.4 - - + -
411B THR* 5.3 0.7 - - + -
439B HIS* 3.9 31.4 - - + -
440B LEU 3.2 23.5 + - - +
441B HIS* 3.8 9.2 - - + +
443B PRO* 1.3 78.4 - - - +
445B GLN* 1.3 58.4 + - - +
447B LEU* 3.3 3.5 + - + +
448B ASP* 2.9 24.4 + - - +
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Residues in contact with GLN 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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301A ASP* 3.5 24.8 + - - +
302A PRO* 4.1 13.7 - - + +
303A SER* 3.8 15.6 + - - -
269B LYS* 4.6 16.5 - - - +
441B HIS* 2.9 19.4 + - - +
442B GLY* 3.4 6.4 - - - +
444B LEU* 1.3 78.0 - - - +
446B TRP* 1.3 68.4 + - + +
448B ASP* 3.1 13.4 + - - +
449B LYS* 2.9 36.1 + - - +
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Residues in contact with TRP 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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338B TYR* 5.0 4.9 - - - -
385B ASN* 3.4 46.0 - - + -
388B PHE* 4.2 15.5 - + - -
389B ALA* 5.5 8.7 - - + -
392B LEU* 4.1 13.2 - - + -
442B GLY* 3.1 23.1 + - - -
443B PRO* 3.3 30.1 - - + +
445B GLN* 1.3 85.1 + - + +
447B LEU* 1.3 63.0 + - - +
449B LYS* 3.2 26.8 + - + +
450B VAL* 3.4 12.3 + - - +
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Residues in contact with LEU 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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300A THR* 3.9 11.0 - - - +
388B PHE* 4.6 4.7 - - + -
392B LEU* 4.1 25.7 - - + +
403B VAL* 3.7 22.4 - - + +
406B LEU* 3.7 10.3 - - + +
407B THR* 3.6 42.6 - - + +
410B CYS* 3.9 10.5 - - - -
443B PRO 2.9 17.9 + - - +
444B LEU* 3.3 6.5 - - + +
446B TRP* 1.3 75.1 - - - +
448B ASP* 1.3 59.8 + - - +
450B VAL* 3.0 2.9 + - - +
451B LEU* 2.8 40.9 + - + +
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Residues in contact with ASP 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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299A PHE* 3.0 18.4 - - - +
300A THR* 3.1 16.5 + - - +
301A ASP* 3.8 15.8 - - + +
308A ARG* 2.5 46.9 + - - -
444B LEU 2.9 9.1 + - - +
445B GLN* 3.1 11.6 + - - +
447B LEU* 1.3 75.9 - - - +
449B LYS* 1.3 61.8 + - + +
450B VAL 2.7 12.3 + - - -
451B LEU* 2.9 14.5 + - - +
452B THR* 3.1 18.3 + - - +
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Residues in contact with LYS 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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301A ASP* 5.0 4.1 + - - -
445B GLN* 2.9 44.2 + - + +
446B TRP* 3.2 16.1 + - + +
448B ASP* 1.3 85.6 + - + +
450B VAL* 1.3 60.1 + - + +
452B THR* 3.1 15.9 + - - -
453B GLN* 4.8 0.7 + - - -
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Residues in contact with VAL 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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392B LEU* 3.7 33.4 - - + +
396B VAL* 5.5 8.7 - - + -
403B VAL* 3.9 22.0 - - + -
446B TRP 3.6 12.3 - - - +
447B LEU 3.0 6.6 + - - +
448B ASP 2.7 4.8 + - - -
449B LYS* 1.3 76.7 - - + +
451B LEU* 1.3 55.2 + - - +
452B THR 3.0 1.8 - - - -
453B GLN* 2.7 49.2 + - + +
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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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298A GLY 5.4 0.9 - - - +
299A PHE* 3.5 31.2 - - + -
300A THR* 3.9 29.6 - - + +
400B PHE* 4.1 24.2 - - + -
403B VAL* 3.8 31.2 - - + -
404B TYR* 4.0 27.1 - - + -
407B THR* 4.5 1.6 - - - +
447B LEU* 2.8 36.7 + - + +
448B ASP* 3.8 4.5 - - - +
450B VAL* 1.3 67.8 - - - +
452B THR* 1.3 56.9 + - - +
453B GLN* 2.8 15.5 + - - +
454B MET* 3.2 10.6 + - - -
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Residues in contact with THR 452 (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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299A PHE* 4.2 7.9 - - + -
308A ARG* 4.1 22.9 - - - +
448B ASP* 3.1 18.0 + - - +
449B LYS* 3.1 21.7 + - - -
451B LEU* 1.3 72.8 - - - +
453B GLN* 1.3 63.5 + - - +
454B MET* 2.9 33.8 - - + +
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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