Contacts of the helix formed by residues 392 - 405 (chain B) in PDB entry 1GKU
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 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387B PRO 2.7 26.0 + - - +
388B ALA* 4.2 14.5 + - + -
391B ARG* 1.3 73.4 - - - +
393B ILE* 1.3 83.5 + - + +
394B ASP* 2.7 10.3 + - + +
395B GLU* 2.6 33.8 + - - +
396B VAL* 3.2 6.4 + - - -
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Residues in contact with ILE 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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366B PRO* 3.4 39.0 - - + -
369B VAL* 3.7 25.6 - - + -
387B PRO* 4.5 12.0 - - + +
391B ARG 4.0 0.2 + - - -
392B HIS* 1.3 96.1 + - + +
394B ASP* 1.3 51.9 + - - +
395B GLU 3.1 0.2 - - - -
396B VAL* 3.4 13.9 - - + +
397B ARG* 2.5 75.9 + - - +
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Residues in contact with ASP 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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362B ASP* 4.4 15.1 - - - +
392B HIS* 2.7 15.0 + - + +
393B ILE* 1.3 77.4 - - - +
395B GLU* 1.3 58.2 + - - +
397B ARG* 3.5 26.7 + - - +
398B GLU* 3.5 9.2 + - - +
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Residues in contact with GLU 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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391B ARG* 2.8 57.9 + - - +
392B HIS 2.6 18.3 + - - +
394B ASP* 1.3 71.2 - - - +
396B VAL* 1.3 55.2 + - - +
397B ARG 3.2 1.8 - - - -
398B GLU* 3.7 5.5 + - + +
399B ILE* 2.8 45.4 + - + +
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Residues in contact with VAL 396 (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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369B VAL* 5.1 16.4 - - + +
370B LYS* 6.1 2.7 - - + -
373B ALA* 6.1 4.3 - - + -
382B ILE* 6.3 2.2 - - + -
385B LEU* 4.3 25.4 - - + -
387B PRO* 4.3 16.6 - - + -
391B ARG* 3.7 17.3 - - + +
392B HIS 3.5 17.7 - - - +
393B ILE* 2.9 18.6 + - + +
395B GLU* 1.3 75.6 - - - +
397B ARG* 1.3 60.2 + - - +
399B ILE* 3.5 9.7 - - + +
400B LEU* 2.8 29.3 + - + +
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Residues in contact with ARG 397 (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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361B ILE* 3.1 44.6 + - + +
362B ASP* 3.8 32.0 + - - +
364B LEU 2.4 33.5 + - - +
365B SER 4.7 0.4 - - - -
369B VAL* 3.5 19.0 - - - +
393B ILE* 2.5 51.7 + - - +
394B ASP* 3.5 20.5 + - - +
396B VAL* 1.3 73.0 - - - +
398B GLU* 1.3 55.3 + - - +
400B LEU* 3.0 6.6 + - - +
401B LYS* 2.5 41.3 + - - +
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Residues in contact with GLU 398 (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 ASP 3.5 9.1 + - - +
395B GLU* 4.0 8.5 - - - +
397B ARG* 1.3 76.1 - - - +
399B ILE* 1.3 64.0 + - + +
401B LYS* 3.9 29.8 + - - +
402B LYS* 2.8 51.4 + - - +
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Residues in contact with ILE 399 (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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377B ARG* 6.2 1.8 - - - +
385B LEU* 5.6 9.9 - - + -
391B ARG* 4.8 16.2 - - - +
395B GLU* 2.8 37.7 - - + +
396B VAL* 3.5 10.5 - - + +
397B ARG 3.1 0.4 - - - -
398B GLU* 1.3 83.2 - - + +
400B LEU* 1.3 62.2 + - - +
402B LYS* 3.6 15.2 - - - +
403B VAL* 3.3 28.1 + - + +
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Residues in contact with LEU 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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361B ILE* 3.8 24.0 - - + -
369B VAL* 3.8 33.4 - - + +
372B LEU* 4.2 12.1 - - + +
373B ALA* 4.5 18.4 - - + +
376B TYR* 4.7 6.1 - - + -
396B VAL* 2.8 21.2 + - + +
397B ARG* 3.3 6.3 - - - +
399B ILE* 1.3 75.8 - - - +
401B LYS* 1.3 66.1 + - - +
403B VAL* 3.3 10.4 - - + +
404B MET* 3.0 46.4 + - + +
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Residues in contact with LYS 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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360B ASP* 5.7 0.9 - - - +
361B ILE* 3.7 32.5 - - + +
362B ASP* 3.0 36.4 + - - -
397B ARG 2.5 24.9 + - - +
398B GLU* 3.4 33.9 + - - +
400B LEU* 1.3 75.6 - - - +
402B LYS* 1.3 65.7 + - - +
404B MET* 3.1 15.9 + - - +
405B GLY* 3.2 10.9 + - - -
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Residues in contact with LYS 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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398B GLU* 2.8 39.1 + - - +
399B ILE* 3.6 17.0 - - - +
401B LYS* 1.3 73.0 - - - +
403B VAL* 1.3 66.3 + - + +
405B GLY 3.6 5.0 + - - +
406B LYS* 3.4 34.6 - - + +
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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
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376B TYR* 4.8 15.7 - - + -
377B ARG* 3.7 32.1 - - + +
399B ILE* 3.3 18.6 - - + +
400B LEU* 3.3 24.5 - - + +
402B LYS* 1.3 79.9 - - + +
404B MET* 1.3 61.5 + - + +
406B LYS* 4.6 4.9 - - + -
407B GLU* 2.7 50.6 + - + +
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Residues in contact with MET 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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358B ILE* 3.4 51.4 - - + -
361B ILE* 4.7 6.5 - - - -
372B LEU* 4.9 5.2 - - + -
376B TYR* 3.7 34.3 + - + +
400B LEU* 3.0 52.7 - - + +
401B LYS* 3.1 5.3 + - - +
403B VAL* 1.3 79.2 - - - +
405B GLY* 1.3 57.8 + - - +
406B LYS 3.1 5.2 + - - -
407B GLU 3.3 13.2 - - - +
416B VAL* 4.7 10.3 - - + -
421B VAL* 4.9 2.2 - - + -
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Residues in contact with GLY 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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401B LYS 3.2 8.9 + - - -
402B LYS 3.7 3.8 - - - +
403B VAL 3.3 0.2 - - - -
404B MET* 1.3 78.0 - - - +
406B LYS* 1.3 61.4 + - - +
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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