Contacts of the helix formed by residues 399 - 405 (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 GLY 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B SER 3.9 0.3 - - - +
396B VAL 3.4 8.6 + - - +
397B ASN* 3.1 6.7 + - - +
398B HIS* 1.3 82.3 - - - +
400B PHE* 1.3 61.1 + - - -
401B GLU* 3.5 2.0 - - - -
402B THR* 3.7 2.9 + - - -
403B VAL* 3.3 22.5 + - - +
453B GLN* 4.2 3.0 + - - -
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Residues in contact with PHE 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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299A PHE* 4.9 11.0 - + - -
328A ARG* 4.3 15.9 - - + -
399B GLY* 1.3 71.0 - - - -
401B GLU* 1.3 65.5 + - - +
402B THR 3.3 0.2 - - - -
403B VAL* 2.8 24.4 - - - +
404B TYR* 2.9 38.5 + + + +
451B LEU* 4.1 30.1 - - + -
453B GLN* 3.4 20.4 - - - +
454B MET* 4.2 0.7 - - - -
455B GLY* 3.8 29.4 - - - -
456B SER* 3.7 35.7 - - - +
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 4.6 26.4 + - - +
399B GLY* 3.5 1.0 - - - -
400B PHE* 1.3 85.3 - - - +
402B THR* 1.3 65.1 + - + +
404B TYR* 3.5 5.5 + - - +
405B GLU* 3.3 25.3 + - + +
458B HIS* 5.2 12.1 + - - -
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Residues in contact with THR 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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395B SER* 4.4 6.5 + - - -
398B HIS* 3.3 53.2 + - + +
399B GLY 3.7 4.1 + - - -
401B GLU* 1.3 81.2 - - + +
403B VAL* 1.3 65.5 + - - +
405B GLU* 3.5 19.9 + - + +
406B LEU* 3.8 11.4 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.4 7.6 - - + -
395B SER* 4.4 14.6 - - - +
396B VAL* 5.4 0.4 - - - +
399B GLY 3.3 6.5 + - - +
400B PHE* 2.8 30.1 - - - +
402B THR* 1.3 78.7 + - - +
404B TYR* 1.3 64.2 + - - +
406B LEU* 3.1 23.9 + - + +
447B LEU* 3.7 15.2 - - + +
450B VAL* 3.9 26.7 - - + -
451B LEU* 3.8 17.7 - - + -
453B GLN* 3.2 26.9 - - - +
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Residues in contact with TYR 404 (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 4.7 10.3 + - - -
300A THR* 5.5 0.4 - - + -
312A GLY* 4.7 13.0 + - - -
324A GLU* 3.8 19.1 + - - -
327A ARG* 3.8 32.0 + - - +
328A ARG* 3.1 52.7 - - + +
400B PHE* 2.9 38.2 + + + +
401B GLU* 3.6 6.3 - - - +
403B VAL* 1.3 78.9 - - - +
405B GLU* 1.3 62.0 + - - +
406B LEU 3.1 0.2 - - - -
407B THR* 2.7 43.0 + - + -
408B LYS* 5.7 0.2 - - - +
451B LEU* 4.0 18.6 - - + -
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Residues in contact with GLU 405 (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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324A GLU* 5.8 1.9 - - - +
328A ARG* 3.9 22.1 + - - +
401B GLU* 3.3 15.2 + - + +
402B THR* 3.5 15.9 - - + +
403B VAL 3.1 0.6 - - - -
404B TYR* 1.3 78.1 - - - +
406B LEU* 1.3 57.9 + - + +
407B THR 3.0 9.6 + - - -
408B LYS* 2.5 66.7 + - - +
409B MET* 4.2 2.9 + - - +
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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