Contacts of the helix formed by residues 313 - 337 (chain G) in PDB entry 4KYI
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 ALA 313 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLU* 1.3 74.8 - - - +
314G GLY* 1.3 54.6 + - - +
315G THR* 3.2 15.0 - - + +
316G ALA* 3.0 9.5 + - + +
317G PHE* 2.6 34.3 + - - +
375G ASN* 4.1 0.2 - - - -
376G THR* 3.3 9.4 - - - +
380G THR* 4.4 15.0 - - + -
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Residues in contact with GLY 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ALA* 1.3 72.1 - - - +
315G THR* 1.3 57.3 + - - +
317G PHE* 3.7 3.4 - - - -
318G GLU* 2.9 43.1 + - - +
375G ASN* 3.3 26.5 + - - -
377G GLY* 4.3 12.8 + - - +
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Residues in contact with THR 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ALA* 4.3 11.3 - - + +
314G GLY* 1.3 76.6 - - - +
316G ALA* 1.3 62.6 + - - +
318G GLU* 5.4 0.4 - - - +
319G ASP* 3.3 25.6 + - - +
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Residues in contact with ALA 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLU* 3.9 21.4 - - + +
313G ALA* 3.0 12.1 + - + +
315G THR* 1.3 82.0 + - - +
317G PHE* 1.3 67.4 + - - +
319G ASP* 3.8 3.5 + - - +
320G ARG* 3.3 21.0 + - - +
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Residues in contact with PHE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLU* 3.3 23.8 + - + +
313G ALA 2.6 21.6 + - - +
314G GLY* 3.1 10.5 + - - +
316G ALA* 1.3 72.7 - - - +
318G GLU* 1.3 74.0 + - + +
320G ARG* 3.0 19.4 + - - +
321G VAL* 3.2 26.6 + - + +
373G TYR* 3.2 30.5 - - + -
374G ILE 4.2 2.2 - - - -
375G ASN* 3.2 46.0 - - + -
397G ASN* 5.2 2.9 - - - -
401G GLN* 3.3 34.3 - - - -
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Residues in contact with GLU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G GLY* 2.9 19.5 + - - +
315G THR* 5.8 0.2 - - - -
317G PHE* 1.3 93.0 - - + +
319G ASP* 1.3 56.7 + - - +
321G VAL* 3.7 6.3 - - - +
322G ASN* 2.9 43.6 + - - +
375G ASN* 4.3 10.3 + - - +
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Residues in contact with ASP 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G THR 3.3 22.7 + - - +
316G ALA* 3.8 4.9 + - - +
317G PHE 3.1 0.6 - - - -
318G GLU* 1.3 78.1 - - - +
320G ARG* 1.3 58.5 + - - +
322G ASN* 3.5 10.8 + - - +
323G LYS* 2.5 60.3 + - - +
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Residues in contact with ARG 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLU* 2.3 42.3 + - - +
316G ALA 3.3 8.8 + - - +
317G PHE* 3.0 18.5 + - - +
319G ASP* 1.3 77.8 - - - +
321G VAL* 1.3 76.8 + - - +
323G LYS* 3.4 12.9 + - - +
324G ALA* 3.1 26.4 + - + +
373G TYR* 3.4 48.3 - - - +
401G GLN* 4.4 7.9 - - - +
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Residues in contact with VAL 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G PHE* 3.2 36.9 + - + +
318G GLU* 3.7 7.4 - - - +
320G ARG* 1.3 94.3 - - - +
322G ASN* 1.3 66.6 + - - +
324G ALA* 3.1 15.7 + - + +
325G LYS* 3.2 33.6 + - + +
401G GLN* 5.4 2.0 - - - +
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Residues in contact with ASN 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G GLU* 2.9 35.3 + - - +
319G ASP* 3.7 11.2 + - - +
321G VAL* 1.3 80.2 - - - +
323G LYS* 1.3 58.5 + - + +
325G LYS* 3.7 1.9 + - - +
326G GLN* 3.1 31.6 + - - +
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Residues in contact with LYS 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319G ASP* 2.5 54.4 + - - +
320G ARG* 3.6 11.4 - - - +
321G VAL 3.3 0.4 - - - -
322G ASN* 1.3 75.3 - - + +
324G ALA* 1.3 59.9 + - - +
326G GLN* 4.0 20.9 - - - +
327G SER* 4.0 13.9 + - - -
361G ARG* 5.6 3.8 - - - -
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Residues in contact with ALA 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ARG* 3.1 13.2 + - + +
321G VAL* 3.3 13.9 - - + +
322G ASN 3.1 0.4 - - - -
323G LYS* 1.3 78.3 - - - +
325G LYS* 1.3 70.0 + - + +
326G GLN 3.1 3.8 - - - -
327G SER* 3.1 19.9 + - - -
328G ALA* 3.1 11.5 + - - +
361G ARG* 6.3 1.6 - - - +
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Residues in contact with LYS 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321G VAL* 3.2 30.0 + - + +
322G ASN* 4.6 2.2 - - - +
324G ALA* 1.3 83.2 - - + +
326G GLN* 1.3 60.2 + - - +
327G SER 3.2 0.2 - - - -
328G ALA* 3.6 13.8 - - + +
329G MET* 2.8 44.8 + - + +
404G GLN* 4.8 13.9 - - - +
556G PHE* 6.0 5.6 - - + -
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Residues in contact with GLN 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G ASN 3.1 18.2 + - - +
323G LYS* 4.0 24.8 - - - +
325G LYS* 1.3 79.1 - - - +
327G SER* 1.3 56.0 + - - +
329G MET* 3.5 7.0 + - + +
330G GLU* 3.2 50.5 + - + +
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Residues in contact with SER 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G LYS 4.0 10.7 + - - -
324G ALA* 3.1 11.0 + - - -
326G GLN* 1.3 76.3 - - - +
328G ALA* 1.3 63.8 + - - +
329G MET 3.2 0.7 - - - -
330G GLU* 3.6 9.4 + - - +
331G ALA* 3.4 18.9 + - - +
360G ASN* 4.5 5.2 + - - +
361G ARG* 3.4 38.9 + - - +
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324G ALA 3.1 12.8 + - - +
325G LYS* 3.7 18.8 - - + +
327G SER* 1.3 76.9 - - - +
329G MET* 1.3 63.2 + - + +
330G GLU 3.5 0.2 - - - -
331G ALA* 3.4 17.8 - - - +
332G ILE* 4.4 8.1 + - - +
543G GLU* 4.6 23.6 - - + +
556G PHE* 5.9 9.3 - - + -
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Residues in contact with MET 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G LYS* 2.8 30.9 + - + +
326G GLN* 3.6 9.6 - - + +
328G ALA* 1.3 77.7 - - + +
330G GLU* 1.3 61.7 + - + +
331G ALA 3.1 5.5 + - - -
332G ILE* 3.4 13.9 + - - +
333G SER* 3.4 15.9 + - - -
556G PHE* 5.3 17.7 - - + -
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Residues in contact with GLU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G GLN* 3.2 38.4 + - + +
327G SER* 3.6 8.3 + - - +
329G MET* 1.3 75.0 - - + +
331G ALA* 1.3 64.3 + - - +
332G ILE 3.3 0.2 - - - -
333G SER* 3.6 13.5 - - - +
334G TRP* 3.0 52.0 + - + +
359G LEU* 4.8 10.4 - - - +
360G ASN* 5.3 1.3 - - - -
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Residues in contact with ALA 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G SER 3.4 12.4 + - - +
328G ALA* 3.4 18.2 - - - +
329G MET 3.1 0.2 - - - -
330G GLU* 1.3 80.8 - - - +
332G ILE* 1.3 60.9 + - + +
334G TRP* 4.6 1.6 - - - +
335G PHE* 3.5 17.7 + - - +
360G ASN* 4.4 17.2 + - - +
539G TRP 4.2 5.9 - - - +
541G PRO* 4.1 25.5 - - + +
542G ILE* 5.2 1.8 - - + +
543G GLU* 5.1 10.1 - - + +
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Residues in contact with ILE 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328G ALA 4.5 9.9 - - - +
329G MET* 3.4 12.6 + - - +
330G GLU 3.3 0.2 - - - -
331G ALA* 1.3 75.6 - - + +
333G SER* 1.3 55.6 + - - +
335G PHE* 3.1 12.8 + - + -
336G LYS* 2.4 65.5 + - + +
541G PRO* 4.5 17.3 - - + -
553G ALA* 5.7 4.3 - - - +
555G ASP* 3.9 17.7 - - + +
556G PHE* 3.1 28.9 - - + +
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Residues in contact with SER 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G MET 3.4 6.2 + - - -
330G GLU* 3.3 25.0 + - - +
332G ILE* 1.3 78.0 - - - +
334G TRP* 1.3 62.9 + - - +
336G LYS* 2.9 23.3 + - - +
337G ALA* 2.9 15.0 + - - +
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Residues in contact with TRP 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G GLU* 3.0 52.8 + - + +
331G ALA 4.6 2.2 - - - +
333G SER* 1.3 80.0 + - - +
335G PHE* 1.3 59.1 + - - +
337G ALA* 3.4 12.4 + - + +
338G ARG* 3.3 21.0 + - - +
356G SER 3.4 29.2 - - - -
359G LEU* 3.8 35.4 + - + +
360G ASN* 5.4 8.3 - - - +
539G TRP* 3.8 33.7 - + + -
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Residues in contact with PHE 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G ALA 3.5 11.2 + - - +
332G ILE* 3.1 19.8 + - + +
333G SER 3.1 0.4 - - - -
334G TRP* 1.3 76.5 - - - +
336G LYS* 1.3 57.2 + - - +
337G ALA 3.0 4.7 - - - -
338G ARG* 4.2 4.5 - - + -
339G MET* 2.8 55.3 + - + +
536G ASN* 3.2 31.6 - - + -
539G TRP* 3.3 34.7 + - + +
540G ALA* 3.7 9.0 - - + -
541G PRO* 3.9 15.9 - - + -
553G ALA* 3.5 36.8 - - + -
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Residues in contact with LYS 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G ILE* 2.4 47.4 + - + +
333G SER* 2.9 11.0 + - - +
335G PHE* 1.3 78.6 - - - +
337G ALA* 1.3 56.1 + - - +
338G ARG 3.3 0.4 - - - -
339G MET* 4.9 8.9 - - - -
340G ASP* 3.0 45.1 - - - +
553G ALA* 3.9 19.8 + - - +
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Residues in contact with ALA 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G SER 2.9 12.7 + - - +
334G TRP* 3.7 16.6 - - + +
335G PHE 3.0 0.8 - - - -
336G LYS* 1.3 78.9 - - - +
338G ARG* 1.3 57.0 + - - +
340G ASP* 4.4 4.2 - - - -
341G SER* 3.7 17.5 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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