Contacts of the helix formed by residues 324 - 334 (chain 6) in PDB entry 3J7Y
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 324 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1946 THR* 3.1 30.9 - - - +
1956 PRO* 3.6 20.9 - - + -
1966 THR* 3.8 16.9 + - + +
3236 TRP* 1.3 100.9 - - - +
3256 ASP* 1.3 85.0 + - - +
3266 SER* 3.3 5.6 - - - +
3276 VAL* 3.2 17.6 + - - +
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Residues in contact with ASP 325 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966 THR* 5.2 2.7 - - + -
3236 TRP* 4.6 4.2 + - - +
3246 ASP* 1.3 87.3 + - - +
3266 SER* 1.3 57.3 + - - +
3286 THR* 2.6 27.1 + - - -
3296 TYR* 3.3 15.0 - - + -
124p LYS* 3.3 34.4 + - - +
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Residues in contact with SER 326 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956 PRO* 3.2 17.5 + - - +
1966 THR* 3.1 44.8 + - - +
1996 ALA* 5.6 4.9 - - - -
3246 ASP* 4.2 0.2 - - - +
3256 ASP* 1.3 76.7 - - - +
3276 VAL* 1.3 62.1 + - - +
3286 THR 3.2 0.7 - - - -
3296 TYR* 3.2 11.8 + - - +
3306 ILE* 2.9 37.3 + - - +
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Residues in contact with VAL 327 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956 PRO* 3.5 31.0 - - + -
2576 PRO 4.4 1.1 - - - +
2586 PHE* 4.1 8.1 - - - -
2596 PRO* 3.4 26.0 - - + +
3236 TRP* 3.3 17.9 - - + -
3246 ASP 3.2 21.7 + - - +
3266 SER* 1.3 76.9 + - - +
3286 THR* 1.3 56.7 + - - +
3306 ILE* 3.2 10.0 + - - +
3316 PHE* 2.9 55.0 + - + -
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Residues in contact with THR 328 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3236 TRP* 3.3 33.2 - - + -
3246 ASP 4.0 0.2 + - - -
3256 ASP 2.6 25.2 + - - +
3276 VAL* 1.3 77.3 - - - +
3296 TYR* 1.3 66.1 + - - +
3316 PHE* 3.2 7.7 + - - +
3326 HIS* 2.9 51.2 + - - +
3396 GLU* 4.2 7.6 - - + +
124p LYS* 3.9 23.1 + - - +
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Residues in contact with TYR 329 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3256 ASP* 3.3 24.7 - - + -
3266 SER* 3.3 12.1 - - - +
3286 THR* 1.3 87.8 + - - +
3306 ILE* 1.3 56.0 + - + +
3326 HIS* 4.8 4.0 - + - -
3336 GLN* 2.8 70.3 + - + +
124p LYS* 6.2 0.4 - - - -
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Residues in contact with ILE 330 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956 PRO* 4.9 0.2 - - + -
1996 ALA* 6.3 0.2 - - + -
2556 LEU* 5.9 0.9 - - + -
2566 PRO* 3.5 35.9 - - + +
2576 PRO 3.5 23.3 - - - +
2586 PHE* 3.8 19.3 - - + -
3266 SER* 2.9 34.1 + - - +
3276 VAL* 3.2 8.9 + - - +
3296 TYR* 1.3 78.5 - - + +
3316 PHE* 1.3 63.1 + - - +
3326 HIS 3.4 0.2 + - - -
3346 LEU* 3.5 22.7 + - + +
3356 LEU* 3.2 45.7 + - + +
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Residues in contact with PHE 331 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2256 LEU* 4.7 7.0 - - + -
2586 PHE* 3.6 39.5 - + + -
2606 ALA* 4.6 12.6 - - + -
3236 TRP* 4.6 1.1 - + - -
3276 VAL* 2.9 45.7 + - + -
3286 THR 3.2 7.6 + - - +
3306 ILE* 1.3 75.8 - - - +
3326 HIS* 1.3 58.8 + - - +
3356 LEU* 3.5 8.9 - - + +
3366 ASP 3.0 24.4 + - - -
3376 MET* 3.4 44.8 + - + +
3396 GLU* 3.5 35.9 - - + -
3406 PRO* 4.1 17.7 - - + -
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Residues in contact with HIS 332 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3286 THR* 2.9 37.1 + - - +
3296 TYR* 4.0 4.0 - + - +
3316 PHE* 1.3 76.6 - - - +
3336 GLN* 1.3 68.6 + - + +
3366 ASP* 3.3 23.7 + - - +
3376 MET 3.6 11.5 + - - +
3396 GLU* 4.3 13.8 - - + +
148W LEU 3.9 14.8 - - - -
128p ASN 5.3 0.8 + - - -
129p ARG* 3.2 56.5 + - + +
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Residues in contact with GLN 333 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3296 TYR* 2.8 56.3 + - + +
3326 HIS* 1.3 76.3 - - + +
3346 LEU* 1.3 70.9 + - + +
3366 ASP* 3.0 17.3 - - - +
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Residues in contact with LEU 334 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2556 LEU* 4.0 13.9 - - + -
2566 PRO* 4.8 9.2 - - + -
2916 TYR* 3.2 67.5 - - + +
3306 ILE* 3.5 30.5 + - + +
3336 GLN* 1.3 95.2 - - + +
3356 LEU* 1.3 71.9 + - + +
3366 ASP* 3.1 16.6 - - - +
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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