Contacts of the helix formed by residues 384 - 395 (chain B) in PDB entry 4KPE
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 ILE 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B ARG* 3.4 19.7 - - + +
381B VAL* 3.0 6.3 + - - +
383B SER* 1.3 90.8 + - - +
385B LEU* 1.3 62.8 + - - -
386B ASP 3.3 2.9 - - - -
387B GLU* 3.1 26.8 + - + +
388B VAL* 2.9 38.4 + - + +
409B TYR* 3.5 41.1 - - + -
411B PHE* 4.1 13.9 - - + -
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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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393A ARG* 3.3 44.4 - - - +
424A LEU* 6.3 0.2 - - + -
381B VAL* 2.8 22.4 + - + +
382B ILE* 3.4 21.5 + - + +
383B SER 3.6 0.8 + - - -
384B ILE* 1.3 76.4 - - - +
386B ASP* 1.3 63.7 + - - +
388B VAL* 3.2 6.4 + - + +
389B ILE* 3.0 37.3 + - + +
427B LEU* 3.9 33.4 - - + +
430B THR* 4.5 13.7 - - - +
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 2.5 43.2 + - - +
384B ILE 3.3 0.6 - - - -
385B LEU* 1.3 78.1 - - - +
387B GLU* 1.3 67.2 + - - +
389B ILE* 3.2 11.1 + - - +
390B ALA* 2.8 30.6 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B SER 4.5 3.5 - - - +
384B ILE* 3.3 33.4 - - + +
386B ASP* 1.3 80.7 + - - +
388B VAL* 1.3 58.1 + - - +
390B ALA* 3.6 7.2 - - - +
391B LEU* 2.9 29.3 + - - +
409B TYR* 3.4 26.8 + - + +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 5.6 2.2 - - + -
381B VAL* 3.9 22.9 - - + -
384B ILE* 2.9 47.8 + - + +
385B LEU* 3.5 8.1 - - + +
387B GLU* 1.3 75.6 - - - +
389B ILE* 1.3 60.7 + - + +
391B LEU* 3.2 5.9 + - - +
392B ILE* 2.9 46.0 + - + +
405B LEU* 4.0 23.1 - - + -
409B TYR* 4.8 4.5 - - + -
419B ILE* 4.3 6.7 - - + -
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 3.9 30.3 - - + -
393A ARG* 4.5 15.5 - - + -
424A LEU* 5.4 6.7 - - + -
427A LEU* 4.3 16.2 - - + -
385B LEU* 3.0 31.1 + - + +
386B ASP* 3.5 11.4 - - - +
388B VAL* 1.3 76.5 - - + +
390B ALA* 1.3 65.1 + - - +
392B ILE* 3.1 9.2 + - - +
393B ARG* 2.8 24.6 + - + +
427B LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 390 (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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386B ASP 2.8 19.8 + - - +
387B GLU* 3.6 9.6 - - - +
389B ILE* 1.3 73.7 - - - +
391B LEU* 1.3 57.9 + - - +
393B ARG* 3.5 8.7 + - - +
394B ALA* 3.0 28.7 + - - +
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Residues in contact with LEU 391 (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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387B GLU 2.9 19.7 + - - +
388B VAL* 3.5 4.0 - - - +
390B ALA* 1.3 73.8 - - - +
392B ILE* 1.3 72.6 + - + +
394B ALA* 3.0 9.8 + - + +
395B SER* 2.7 25.2 + - - +
401B ALA 4.1 2.9 - - - +
404B ASN* 3.8 44.4 + - + +
405B LEU* 3.8 29.2 - - + -
408B SER* 4.0 18.4 - - - +
409B TYR* 4.2 13.7 - - + -
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Residues in contact with ILE 392 (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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424A LEU* 3.9 49.1 - - + +
425A TYR* 4.2 6.7 - - - -
427A LEU* 4.5 7.2 - - + -
428A THR* 3.2 32.3 - - + +
388B VAL* 2.9 38.1 + - + +
389B ILE* 3.7 6.3 - - - +
391B LEU* 1.3 84.1 - - + +
393B ARG* 1.3 65.8 + - - +
395B SER* 2.9 16.3 + - - -
401B ALA* 4.4 11.9 - - + -
405B LEU* 4.6 2.7 - - + -
419B ILE* 4.5 5.2 - - + -
420B VAL* 4.5 12.1 - - + -
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Residues in contact with ARG 393 (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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385A LEU* 3.5 29.2 - - - +
386A ASP* 2.7 48.3 + - - -
389A ILE* 4.1 24.2 - - + -
427A LEU* 3.9 26.5 + - + +
428A THR 4.6 2.6 + - - +
429A ASN 5.3 0.8 + - - -
430A THR* 4.5 21.2 + - - +
389B ILE* 2.8 18.8 + - + +
390B ALA* 3.6 11.9 - - - +
392B ILE* 1.3 73.0 - - - +
394B ALA* 1.3 61.0 + - - +
395B SER 3.5 6.1 + - - +
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Residues in contact with ALA 394 (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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390B ALA 3.0 18.4 + - - +
391B LEU* 3.0 10.2 + - + +
393B ARG* 1.3 76.0 - - - +
395B SER* 1.3 61.8 + - - +
404B ASN* 5.2 2.5 - - - +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR* 3.4 19.7 - - - +
391B LEU 2.7 16.1 + - - -
392B ILE* 2.9 12.1 + - - -
393B ARG 3.6 6.1 - - - +
394B ALA* 1.3 81.3 - - - +
396B GLU* 1.3 63.9 + - - +
400B ASP* 3.4 14.8 - - - -
401B ALA* 3.4 31.2 - - - -
404B ASN* 3.2 16.4 + - - +
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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