Contacts of the helix formed by residues 390 - 401 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LYS* 3.5 12.8 - - - +
5D ASN* 2.8 34.2 + - - +
383D MET 4.5 0.6 - - - +
384D PHE* 5.0 0.9 - - - -
387D GLY* 2.9 20.9 + - - +
388D LYS 3.4 1.0 + - - +
389D GLY* 1.3 77.1 - - - +
391D LEU* 1.3 57.3 + - - +
392D ALA* 2.8 17.0 + - - +
393D ILE* 3.0 27.8 + - + +
394D GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 4.4 15.5 + - - +
235D THR* 3.9 26.0 - - + +
238D LEU* 3.7 41.5 - - + -
239D LEU* 4.4 6.3 - - + -
380D LEU* 4.9 2.9 - - + -
383D MET* 4.0 37.2 - - + -
384D PHE* 3.8 32.5 - - + -
389D GLY 3.7 4.0 + - - -
390D ASP* 1.3 71.1 + - - +
392D ALA* 1.3 62.2 + - - +
394D GLY* 3.7 2.2 - - - +
395D THR* 2.8 33.4 + - - -
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Residues in contact with ALA 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.8 32.8 - - + -
5D ASN* 4.1 16.3 - - + +
191D LEU* 3.7 9.0 - - + +
195D GLN* 4.8 2.0 - - - +
239D LEU* 4.1 16.9 - - + +
390D ASP* 2.8 9.4 + - - +
391D LEU* 1.3 76.3 - - - +
393D ILE* 1.3 65.3 + - - +
395D THR* 3.2 14.0 + - - -
396D VAL* 3.2 17.7 + - - +
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.6 29.2 - - + +
4D LYS* 3.8 22.2 - - + +
387D GLY* 4.1 11.4 - - - +
390D ASP* 3.0 28.5 + - + +
392D ALA* 1.3 74.8 - - - +
394D GLY* 1.3 62.2 + - - +
396D VAL* 3.3 10.3 + - + +
397D LYS* 3.1 47.2 + - + +
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Residues in contact with GLY 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D MET* 3.2 32.8 - - - +
386D LEU* 4.4 3.3 - - - +
387D GLY* 3.5 9.8 - - - -
390D ASP 2.9 14.9 + - - -
391D LEU 3.7 2.0 - - - -
392D ALA 3.2 0.2 - - - -
393D ILE* 1.3 76.5 - - - +
395D THR* 1.3 56.8 + - - +
397D LYS* 3.7 1.0 - - - +
398D ALA* 2.8 31.5 + - - +
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Residues in contact with THR 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.7 33.0 - - + -
187D ILE* 4.1 2.5 - - + -
191D LEU* 4.0 15.9 - - + -
235D THR* 3.5 11.1 - - - +
239D LEU* 4.7 0.9 - - - +
383D MET* 3.3 24.3 - - + +
391D LEU 2.8 25.1 + - - -
392D ALA* 3.2 6.3 + - - -
394D GLY* 1.3 73.7 - - - +
396D VAL* 1.3 66.6 + - - +
398D ALA* 3.3 2.2 + - - +
399D PHE* 3.0 35.7 + - + -
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Residues in contact with VAL 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.8 21.1 - - + -
187D ILE* 4.2 10.4 - - + +
188D GLU* 3.9 36.6 - - + +
191D LEU* 3.9 5.4 - - + -
392D ALA 3.2 12.9 + - - +
393D ILE* 3.3 9.2 + - + +
395D THR* 1.3 79.2 - - - +
397D LYS* 1.3 60.0 + - + +
399D PHE* 3.3 3.3 + - - +
400D GLU* 3.1 46.7 + - + +
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Residues in contact with LYS 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D LEU* 3.2 45.8 - - + +
388D LYS* 6.3 2.2 - - - +
393D ILE* 3.1 36.6 + - + +
394D GLY 3.9 0.2 - - - +
396D VAL* 1.3 76.2 - - + +
398D ALA* 1.3 55.0 + - - +
400D GLU* 3.3 19.9 + - - +
401D THR* 2.7 43.2 + - + +
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Residues in contact with ALA 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D MET* 3.7 23.6 - - + -
386D LEU* 3.8 6.7 - - + +
394D GLY 2.8 18.6 + - - +
395D THR* 3.7 6.3 - - - +
397D LYS* 1.3 77.8 - - - +
399D PHE* 1.3 62.2 + - - +
401D THR* 3.3 5.9 + - - -
402D GLY 3.0 3.5 + - - -
403D VAL* 2.9 40.3 + - + -
404D MET* 3.4 13.9 + - + +
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Residues in contact with PHE 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.6 29.2 - - + -
179D VAL* 3.7 16.6 - - + -
187D ILE* 3.9 24.2 - - + -
395D THR* 3.0 32.9 + - + +
396D VAL 3.8 5.8 - - - +
398D ALA* 1.3 73.1 - - - +
400D GLU* 1.3 68.4 + - - +
401D THR 3.2 0.7 + - - -
402D GLY* 3.3 9.5 + - - -
404D MET* 3.5 51.2 - - + +
406D ILE* 4.2 8.5 - - + -
413D TYR* 3.6 30.6 - - + +
414D ASN* 3.6 23.8 - - - -
415D ALA* 4.5 6.9 + - - +
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Residues in contact with GLU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D VAL* 3.1 33.6 + - + +
397D LYS* 3.6 29.2 + - - +
399D PHE* 1.3 78.3 - - - +
401D THR* 1.3 64.3 + - + +
413D TYR* 5.1 7.4 - - + -
415D ALA* 5.9 0.9 - - - +
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Residues in contact with THR 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D LEU* 3.8 12.4 - - + +
397D LYS* 2.7 27.6 + - + +
398D ALA* 3.5 1.6 + - - -
400D GLU* 1.3 83.1 - - + +
402D GLY* 1.3 54.3 + - - +
403D VAL* 3.4 21.1 + - - +
415D ALA* 5.4 0.4 - - - -
435D ASN* 2.8 34.9 + - - +
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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