Contacts of the helix formed by residues 272 - 287 (chain J) in PDB entry 3FKS
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 272 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J LYS* 5.3 1.9 + - - -
208J VAL* 3.6 14.2 + - - +
270J TYR* 3.5 2.2 - - - -
271J ASP* 1.3 90.1 + - - +
273J LEU* 1.3 61.9 + - - +
274J SER* 3.2 11.8 + - - -
275J LYS* 2.8 70.3 + - - +
276J GLN* 3.4 10.6 + - - +
328J VAL* 3.0 30.2 - - + +
330J GLU* 4.7 10.1 - - - +
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Residues in contact with LEU 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249J PRO* 4.7 3.4 - - + -
270J TYR* 3.5 28.7 + - + -
272J ASP* 1.3 72.9 - - - +
274J SER* 1.3 59.2 + - - +
275J LYS 3.3 0.2 - - - -
276J GLN* 3.5 22.4 - - + +
277J ALA* 2.9 26.7 + - - +
304J HIS* 3.3 31.0 + - + +
307J LEU* 3.8 19.1 - - + -
308J LEU* 4.6 10.3 - - + -
327J PRO* 3.6 30.5 - - + -
328J VAL 3.2 4.1 + - - +
329J ILE* 3.7 13.7 - - + -
344J VAL* 4.4 14.4 - - + -
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Residues in contact with SER 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J ASP* 3.1 9.6 - - - -
273J LEU* 1.3 81.3 - - - +
275J LYS* 1.3 60.9 + - - +
276J GLN 3.5 0.3 + - - -
277J ALA* 3.7 2.9 + - - +
278J VAL* 3.2 26.7 + - - +
296J TYR* 4.7 1.4 + - - -
329J ILE* 3.4 17.2 - - - +
330J GLU* 2.9 41.6 + - - -
340J ILE* 4.7 10.0 - - - +
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Residues in contact with LYS 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J VAL* 3.4 26.7 - - - +
209J GLY* 3.8 22.5 + - - +
210J GLN* 4.5 14.1 - - - +
245J GLN* 3.9 8.9 - - - +
271J ASP* 5.0 1.0 + - - -
272J ASP* 2.8 31.5 + - - +
274J SER* 1.3 76.8 - - - +
276J GLN* 1.3 61.8 + - - +
278J VAL* 4.0 10.3 - - + +
279J ALA* 3.5 17.5 + - - +
330J GLU* 4.2 20.8 + - - -
327M ALA* 3.8 26.4 - - - +
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Residues in contact with GLN 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J VAL* 4.3 7.4 - - + -
245J GLN 3.9 11.4 - - - +
246J TYR* 3.5 18.0 + - + +
249J PRO* 3.3 41.0 - - + +
250J PHE* 3.9 17.0 - - - -
272J ASP 3.4 11.7 + - - +
273J LEU* 3.2 12.0 + - - +
274J SER 3.2 0.6 - - - -
275J LYS* 1.3 76.2 - - - +
277J ALA* 1.3 63.6 + - - +
278J VAL 3.1 2.0 - - - -
279J ALA* 3.1 6.5 + - - +
280J TYR* 3.1 21.5 + - - +
303J LEU* 4.3 12.8 - - - +
304J HIS* 3.1 31.4 + - - -
307J LEU* 4.6 2.9 - - - +
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Residues in contact with ALA 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273J LEU 2.9 16.6 + - - +
274J SER 4.0 4.9 - - - +
275J LYS 3.5 0.2 - - - -
276J GLN* 1.3 78.1 + - - +
278J VAL* 1.3 56.0 + - - +
280J TYR* 3.6 2.8 + - - +
281J ARG* 3.0 26.5 + - - +
296J TYR* 3.5 10.9 - - + -
300J VAL* 4.3 7.2 - - + +
303J LEU* 4.6 11.2 - - - -
304J HIS* 3.8 17.9 - - + -
340J ILE* 3.9 26.0 - - + -
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Residues in contact with VAL 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J SER 3.2 19.7 + - - +
275J LYS* 4.0 8.7 - - - +
276J GLN 3.1 0.4 - - - -
277J ALA* 1.3 75.6 - - - +
279J ALA* 1.3 59.7 + - - +
281J ARG* 3.0 30.5 + - - +
282J GLN* 2.9 28.9 + - + +
296J TYR* 3.6 18.8 - - - +
283M PRO 5.9 2.0 - - - +
286M ALA* 3.9 26.7 - - + -
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Residues in contact with ALA 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J ALA* 3.7 28.4 - - - +
245J GLN* 4.0 19.7 - - + +
246J TYR* 4.4 5.6 - - - +
275J LYS 3.5 12.2 + - - +
276J GLN 3.1 11.3 + - - +
278J VAL* 1.3 79.8 - - - +
280J TYR* 1.3 59.5 + - - +
282J GLN* 3.3 17.2 + - - +
283J LEU* 3.3 19.4 + - - +
286M ALA* 6.2 1.3 - - - -
287M THR* 6.3 1.3 - - + -
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Residues in contact with TYR 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J LEU* 5.8 7.0 - - + -
246J TYR* 3.4 42.1 - + + +
276J GLN 3.1 11.9 + - - +
277J ALA 3.9 2.9 - - - +
279J ALA* 1.3 77.4 - - - +
281J ARG* 1.3 58.5 + - - +
283J LEU* 3.7 13.6 + - + +
284J SER* 3.0 30.1 + - - -
289J ARG* 3.4 21.9 + - - -
297J PRO* 3.4 23.5 - - + +
299J ASP* 2.7 49.5 + - - -
300J VAL* 4.7 4.3 - - + -
303J LEU* 3.9 28.9 - - + -
306J ARG* 5.4 4.6 + - - -
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Residues in contact with ARG 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ALA 3.0 15.3 + - - +
278J VAL* 3.0 32.1 + - - +
280J TYR* 1.3 76.0 - - - +
282J GLN* 1.3 59.8 + - - +
285J LEU* 2.9 42.1 + - + +
294J GLU* 3.4 16.3 + - - +
295J ALA* 3.2 34.8 - - - +
296J TYR* 3.7 37.9 + - + -
297J PRO* 4.0 8.3 - - + -
277M SER* 3.3 22.9 + - - -
278M ALA* 3.6 14.3 - - - +
282M GLN 5.8 0.4 + - - -
283M PRO* 5.9 2.4 + - - +
285M LEU* 6.2 3.8 - - - +
320M PRO* 5.8 5.5 - - - +
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Residues in contact with GLN 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J ASP 5.1 2.8 + - - -
39J GLY* 6.1 1.4 - - - -
242J ALA* 3.6 21.5 - - + +
278J VAL* 2.9 12.0 + - + +
279J ALA* 3.5 10.0 - - - +
281J ARG* 1.3 77.5 - - - +
283J LEU* 1.3 67.7 + - + +
285J LEU* 3.9 0.7 - - - +
286J LEU* 2.9 45.6 + - + +
283M PRO* 3.2 33.6 - - - +
284M THR* 3.8 13.2 - - - +
286M ALA* 5.1 3.0 - - + +
287M THR* 3.2 41.1 + - - +
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Residues in contact with LEU 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J GLY 5.8 2.0 - - - +
40J ILE* 5.7 3.4 - - + -
66J LEU* 4.2 23.1 - - + -
76J VAL* 3.8 19.7 - - + -
242J ALA* 3.9 8.5 - - + -
243J PRO* 3.8 49.4 - - + -
246J TYR* 4.4 17.7 - - + -
279J ALA 3.3 12.4 + - - +
280J TYR* 3.9 13.7 - - + +
282J GLN* 1.3 83.3 - - + +
284J SER* 1.3 64.8 + - - +
286J LEU* 3.7 5.5 - - + +
287J LEU* 3.0 31.5 + - + +
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Residues in contact with SER 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280J TYR* 3.0 26.7 + - - -
281J ARG 3.6 3.6 - - - -
282J GLN 3.3 0.2 - - - -
283J LEU* 1.3 76.5 - - - +
285J LEU* 1.3 63.2 + - - +
287J LEU* 3.1 7.0 + - - +
289J ARG* 3.1 56.2 + - - +
290J PRO 4.8 0.2 + - - -
297J PRO* 3.2 36.7 - - - +
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Residues in contact with LEU 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J ARG* 2.9 39.8 + - + +
282J GLN 3.9 2.7 - - - +
284J SER* 1.3 74.6 - - - +
286J LEU* 1.3 59.5 + - - +
287J LEU 3.0 0.2 - - - -
288J ARG* 2.9 18.9 + - - +
289J ARG 4.5 5.8 - - - +
291J PRO* 3.8 18.2 - - + -
295J ALA* 3.7 22.0 - - + +
275M ILE* 3.5 45.9 - - + +
276M PRO 4.6 0.4 - - - +
277M SER* 3.9 31.9 - - - +
283M PRO* 4.1 21.1 - - + -
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Residues in contact with LEU 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J ASP* 3.4 39.0 - - + +
40J ILE* 3.1 26.7 - - + +
282J GLN* 2.9 41.2 + - + +
283J LEU* 3.9 4.3 - - + +
285J LEU* 1.3 75.5 - - - +
287J LEU* 1.3 56.3 + - - +
288J ARG* 3.2 11.4 + - - +
274M ARG* 4.3 23.6 - - + +
275M ILE 5.5 1.3 - - - +
283M PRO* 4.2 22.2 - - + -
284M THR* 3.9 15.5 - - + -
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Residues in contact with LEU 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ILE* 3.8 30.1 - - + -
42J ARG* 6.4 0.4 - - + -
66J LEU* 4.0 24.7 - - + -
67J ASN* 3.3 53.0 + - + +
69J GLU* 5.1 2.0 - - - +
74J GLY* 4.6 10.3 - - - -
76J VAL* 4.2 16.4 - - + -
283J LEU* 3.0 21.9 + - + +
284J SER* 3.6 4.9 - - - +
285J LEU 3.0 0.8 - - - -
286J LEU* 1.3 75.3 - - - +
288J ARG* 1.3 64.1 + - - +
289J ARG* 3.0 18.8 + - + +
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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
------------------------------------------------------------
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