Contacts of the helix formed by residues 380 - 387 (chain B) in PDB entry 4KMH
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 380 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLN* 4.3 17.3 - - - +
266B LEU* 4.6 5.6 - - + -
269B VAL* 3.6 42.0 - - + -
271B ALA* 5.6 0.9 - - + -
376B GLU 4.0 12.6 - - - +
377B SER* 3.5 10.1 - - - +
378B GLY 3.1 1.2 - - - -
379B ALA* 1.3 78.9 - - + +
381B ILE* 1.3 52.3 + - - +
382B PRO 3.4 1.8 - - - -
383B LEU* 3.1 33.1 + - + +
384B CYS* 2.8 33.4 + - - +
395B PHE* 4.7 6.5 - - + -
397B TYR* 3.3 14.8 - - + +
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Residues in contact with ILE 381 (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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373B PHE* 3.6 35.2 - - + -
377B SER 4.2 0.2 - - - +
378B GLY* 3.4 24.7 - - - +
380B LEU* 1.3 76.5 - - - +
382B PRO* 1.4 62.2 - - + +
384B CYS* 3.1 7.0 + - + +
385B LEU* 2.8 39.0 + - + +
397B TYR* 3.2 19.2 + - + +
408B PHE* 5.6 7.2 - - + -
443B MET* 5.8 1.6 - - + -
447B LEU* 3.8 27.8 - - + -
450B LEU* 4.3 5.6 - - + -
471B VAL* 4.3 9.2 - - + -
473B ILE* 3.9 11.2 - - + -
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Residues in contact with PRO 382 (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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378B GLY 3.9 4.7 - - - +
379B ALA 3.6 17.0 - - - +
381B ILE* 1.4 94.5 - - + +
383B LEU* 1.3 52.9 + - - +
386B ARG* 2.6 60.6 + - - +
444B LEU* 4.2 15.2 - - + +
447B LEU* 5.3 10.3 - - + +
449B ASP* 6.0 0.9 - - - +
450B LEU* 4.5 25.8 - - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 3.8 29.2 - - + +
259B ILE* 3.8 24.5 - - + -
264B SER* 3.2 38.8 - - - +
266B LEU* 4.1 12.6 - - + -
379B ALA 5.0 1.5 + - - +
380B LEU* 3.1 38.3 + - + +
382B PRO* 1.3 78.8 - - - +
384B CYS* 1.3 58.9 + - - +
386B ARG* 4.9 0.4 - - - -
387B GLY* 2.9 31.7 + - - +
388B ARG* 3.5 3.6 + - + +
395B PHE* 5.3 3.4 - - + -
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Residues in contact with CYS 384 (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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380B LEU 2.8 16.3 + - - +
381B ILE* 3.3 11.9 - - - +
383B LEU* 1.3 74.9 - - - +
385B LEU* 1.3 62.0 + - - +
388B ARG* 3.1 31.4 - - - +
389B LEU* 3.2 8.2 + - - +
395B PHE* 3.8 31.9 - - + -
397B TYR* 4.0 8.5 - - - +
408B PHE* 3.7 42.0 - - - -
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Residues in contact with LEU 385 (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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381B ILE* 2.8 27.3 + - + +
384B CYS* 1.3 75.9 - - - +
386B ARG* 1.3 61.0 + - - +
389B LEU* 3.4 30.3 + - + +
390B LEU* 2.9 34.7 + - - +
408B PHE* 4.3 11.9 - - + -
435B LEU* 4.1 11.2 - - + -
440B VAL* 4.1 17.0 - - + +
443B MET* 4.4 15.9 - - + -
444B LEU* 3.9 28.7 - - + -
447B LEU* 3.9 28.0 - - + -
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Residues in contact with ARG 386 (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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256B ASP 5.8 2.0 - - - -
259B ILE* 4.2 5.6 - - + +
260B GLU* 3.9 42.6 + - + +
382B PRO* 2.6 36.5 + - - +
383B LEU* 4.9 1.1 - - - -
385B LEU* 1.3 74.0 - - - +
387B GLY* 1.3 55.8 + - - +
390B LEU* 3.5 32.4 - - + +
391B HIS* 3.5 11.1 + - - -
444B LEU* 3.9 42.3 + - + +
447B LEU 5.1 3.8 + - - -
448B GLU* 6.3 0.4 - - - -
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Residues in contact with GLY 387 (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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259B ILE* 3.5 28.9 - - - +
263B GLY* 3.5 0.3 - - - -
264B SER* 2.9 23.0 + - - -
383B LEU 2.9 12.5 + - - -
386B ARG* 1.3 77.5 - - - +
388B ARG* 1.3 67.3 + - - +
391B HIS* 3.5 13.1 - - - -
393B ARG* 4.0 3.6 + - - -
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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