Contacts of the helix formed by residues 390 - 401 (chain B) in PDB entry 1CCW
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 ASP 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LYS* 3.5 11.3 - - - +
5B ASN* 2.7 29.5 + - - +
383B MET 4.5 1.0 - - - +
384B PHE* 4.8 0.7 - - - -
387B GLY* 3.0 19.3 + - - +
388B LYS 3.4 1.4 + - - +
389B GLY* 1.3 76.2 - - - +
391B LEU* 1.3 58.4 + - - +
392B ALA* 2.9 35.0 + - - +
393B ILE* 3.0 27.0 + - + +
394B GLY* 2.9 24.1 + - - -
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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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5B ASN* 4.3 14.3 + - - +
235B THR* 3.9 26.5 - - + +
238B LEU* 3.6 42.0 - - + -
239B LEU* 4.4 6.1 - - + -
380B LEU* 4.9 2.5 - - + -
383B MET* 3.9 35.9 - - + -
384B PHE* 3.8 34.0 - - + -
389B GLY 3.7 4.6 + - - -
390B ASP* 1.3 73.4 + - - +
392B ALA* 1.3 58.1 + - - +
394B GLY* 4.3 1.8 - - - +
395B THR* 2.8 32.7 + - - -
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Residues in contact with ALA 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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3B LEU* 3.9 31.4 - - + -
4B LYS 4.7 0.2 - - - +
5B ASN* 4.0 17.4 - - + +
191B LEU* 3.6 8.6 - - + +
195B GLN* 4.8 1.6 - - - +
239B LEU* 4.0 17.3 - - + +
390B ASP* 2.9 9.0 + - - +
391B LEU* 1.3 73.9 - - - +
393B ILE* 1.4 67.9 + - - +
395B THR* 3.1 15.3 + - - -
396B VAL* 3.2 16.6 + - - +
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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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3B LEU* 3.6 33.2 - - + +
4B LYS* 4.8 5.6 - - + -
387B GLY* 4.1 10.3 - - - +
390B ASP* 3.0 32.1 + - + +
392B ALA* 1.4 75.0 - - - +
394B GLY* 1.3 62.6 + - - +
396B VAL* 3.3 7.2 + - + +
397B LYS* 3.1 49.0 + - + +
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Residues in contact with GLY 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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383B MET* 3.2 32.5 - - - +
386B LEU* 4.3 3.8 - - - +
387B GLY* 3.6 11.8 - - - -
390B ASP 2.9 12.8 + - - -
391B LEU 3.4 2.2 + - - -
393B ILE* 1.3 76.2 - - - +
395B THR* 1.3 56.4 + - - +
397B LYS* 3.4 1.6 + - - +
398B ALA* 2.8 31.5 + - - +
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Residues in contact with THR 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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175B ILE* 3.7 33.4 - - + -
187B ILE* 4.0 7.0 - - + -
191B LEU* 3.9 16.4 - - + -
235B THR* 3.6 11.1 - - - +
239B LEU* 4.8 0.7 - - - +
383B MET* 3.3 24.2 - - + +
391B LEU 2.8 21.4 + - - -
392B ALA* 3.1 9.7 + - - -
394B GLY* 1.3 74.5 - - - +
396B VAL* 1.3 67.7 + - - +
398B ALA* 3.2 1.7 + - - +
399B PHE* 3.0 30.6 + - + -
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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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3B LEU* 3.8 21.1 - - + -
187B ILE* 4.1 12.0 - - + +
188B GLU* 3.9 33.7 - - + +
191B LEU* 3.9 10.1 - - + -
392B ALA 3.2 12.9 + - - +
393B ILE* 3.3 8.3 + - + +
395B THR* 1.3 76.8 - - - +
397B LYS* 1.3 65.2 - - + +
399B PHE* 3.3 3.6 + - - +
400B GLU* 3.1 41.5 + - + +
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Residues in contact with LYS 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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386B LEU* 3.3 41.3 - - + +
388B LYS* 5.4 7.3 - - - +
393B ILE* 3.1 36.1 + - + +
394B GLY 4.0 2.9 - - - +
396B VAL* 1.3 75.5 - - + +
398B ALA* 1.3 63.6 + - - +
400B GLU* 3.2 19.7 + - - +
401B THR* 2.9 34.7 + - + +
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Residues in contact with ALA 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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383B MET* 3.8 23.6 - - + -
386B LEU* 3.8 7.1 - - + +
394B GLY 2.8 18.3 + - - +
395B THR* 3.6 6.3 - - - +
397B LYS* 1.3 78.7 - - - +
399B PHE* 1.3 56.4 + - - +
401B THR* 3.4 6.1 + - - -
402B GLY 3.0 8.7 + - - -
403B VAL* 2.9 32.5 + - + -
404B MET* 3.4 22.0 + - + +
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Residues in contact with PHE 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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175B ILE* 3.7 28.3 - - + -
179B VAL* 3.9 14.6 - - + -
187B ILE* 3.9 26.9 - - + -
395B THR* 3.0 31.2 + - + +
396B VAL 3.7 7.2 - - - +
398B ALA* 1.3 75.2 - - - +
400B GLU* 1.3 65.5 + - + +
401B THR 3.2 0.7 + - - -
402B GLY* 3.4 9.9 + - - -
404B MET* 3.5 51.6 - - + -
406B ILE* 4.2 7.6 - - + -
413B TYR* 3.5 30.1 - - + +
414B ASN* 3.5 25.1 - - - -
415B ALA* 4.5 7.6 + - - +
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Residues in contact with GLU 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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396B VAL* 3.1 31.3 + - + +
397B LYS* 3.2 29.0 + - - +
399B PHE* 1.3 77.7 - - - +
401B THR* 1.3 64.0 + - + +
413B TYR* 5.1 6.7 - - + -
415B ALA* 5.9 0.9 - - - +
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Residues in contact with THR 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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382B LYS* 5.9 0.2 - - - -
386B LEU* 3.8 16.3 - - + +
397B LYS* 2.9 24.0 + - + +
398B ALA 3.5 4.5 + - - -
399B PHE 3.2 0.2 - - - -
400B GLU* 1.3 82.7 - - + +
402B GLY* 1.3 56.6 + - - +
403B VAL* 3.4 18.8 + - - +
435B ASN* 2.9 31.0 + - - +
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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