Contacts of the helix formed by residues 387 - 407 (chain C) 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 THR 387 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C SER 4.4 0.2 + - - -
386C PRO* 1.3 72.4 - - - +
388C PRO* 1.3 77.0 - - - +
389C GLU* 3.1 22.5 + - + +
390C GLN* 3.1 51.5 + - + +
391C ARG* 3.4 4.2 - - - +
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Residues in contact with PRO 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PRO 3.7 3.8 - - - +
387C THR* 1.3 88.9 - - - +
389C GLU* 1.3 70.9 + - + +
390C GLN 3.1 2.4 + - - -
391C ARG* 3.9 16.7 - - + +
392C ALA* 3.4 22.7 + - - +
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Residues in contact with GLU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C THR* 3.1 15.8 - - + +
388C PRO* 1.3 87.5 - - + +
390C GLN* 1.3 57.5 + - - +
392C ALA* 4.5 5.5 - - - +
393C ARG* 4.2 12.3 + - - +
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Residues in contact with GLN 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C GLU* 2.4 47.4 + - - +
379C VAL* 3.8 17.7 - - + +
386C PRO* 3.2 16.3 - - + +
387C THR* 3.1 51.2 + - + +
389C GLU* 1.3 76.7 - - - +
391C ARG* 1.3 61.6 + - - +
392C ALA 3.3 2.0 - - - -
393C ARG* 3.2 12.2 + - + +
394C ALA* 3.0 25.3 + - - +
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 3.6 44.1 - - + +
96C GLU* 3.4 35.4 + - - +
99C ASP* 3.7 21.1 + - - +
100C ILE* 6.2 0.2 - - - +
379C VAL* 4.4 7.0 - - + -
386C PRO* 3.7 33.1 - - + +
387C THR 3.4 16.4 - - - +
388C PRO* 3.5 14.5 + - + +
390C GLN* 1.3 76.6 - - + +
392C ALA* 1.3 63.7 + - - +
394C ALA* 3.2 10.4 + - - +
395C VAL* 3.1 26.8 + - - +
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Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C PRO 3.4 14.6 + - - +
389C GLU* 4.8 5.4 - - - +
390C GLN 3.3 0.4 - - - -
391C ARG* 1.3 78.8 - - - +
393C ARG* 1.3 61.7 + - - +
395C VAL* 3.3 11.6 + - - +
396C LYS* 3.1 21.5 + - - +
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Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ASN* 5.9 0.2 - - - +
389C GLU 4.2 6.6 + - - +
390C GLN* 3.2 22.2 + - + +
392C ALA* 1.3 77.1 - - - +
394C ALA* 1.3 64.0 + - - +
396C LYS* 3.1 45.1 + - + +
397C ASN* 2.6 59.2 + - - +
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Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 5.1 4.9 - - + +
49C SER* 4.6 21.5 - - - +
374C ILE* 4.9 1.4 - - - +
375C ASN 4.9 5.5 - - - +
376C THR 4.7 6.7 - - - +
377C GLY* 6.0 1.8 - - - -
379C VAL* 3.8 22.4 - - + -
390C GLN 3.0 12.5 + - - +
391C ARG* 3.2 10.5 + - - +
393C ARG* 1.3 78.1 - - - +
395C VAL* 1.3 61.0 + - + +
397C ASN* 3.2 11.8 - - - +
398C GLY* 3.1 18.0 + - - -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 3.8 27.4 - - + +
49C SER 5.5 0.2 - - - -
51C LEU* 3.7 22.4 - - + -
52C GLY* 3.5 28.3 - - - +
55C GLN* 4.5 7.2 - - - +
96C GLU* 5.9 3.8 - - + +
391C ARG 3.1 17.3 + - - +
392C ALA* 3.5 11.0 - - - +
393C ARG 3.2 0.2 - - - -
394C ALA* 1.3 73.2 - - - +
396C LYS* 1.3 64.4 + - - +
398C GLY* 3.1 2.4 + - - +
399C TYR* 3.0 21.1 + - + +
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Residues in contact with LYS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ALA 3.1 12.9 + - - +
393C ARG* 3.1 46.6 + - + +
395C VAL* 1.3 77.3 - - - +
397C ASN* 1.3 56.2 + - - +
399C TYR* 4.3 6.5 - - + -
400C ASP* 2.8 60.2 + - - +
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Residues in contact with ASN 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C PHE* 4.9 3.0 - - - -
374C ILE* 4.8 2.2 - - + -
375C ASN* 3.8 46.8 + - + +
377C GLY* 5.4 3.3 + - - -
393C ARG* 2.6 45.5 + - - +
394C ALA* 3.2 13.7 - - - +
396C LYS* 1.3 76.8 - - - +
398C GLY* 1.3 57.9 + - - +
400C ASP* 5.0 2.1 - - - +
401C GLN* 2.9 54.7 + - - +
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C SER 4.3 4.9 - - - -
52C GLY* 3.6 7.4 - - - -
53C MET* 3.3 11.9 - - - -
374C ILE* 3.8 27.3 - - - +
394C ALA 3.1 9.9 + - - -
395C VAL 3.1 3.3 + - - -
397C ASN* 1.3 77.9 - - - +
399C TYR* 1.3 56.0 + - - +
402C THR* 2.4 31.8 + - - -
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY* 3.3 19.5 + - - +
55C GLN* 4.2 17.0 - - + +
56C ALA* 3.8 22.7 - - + -
59C GLU* 2.3 39.5 + - - -
395C VAL* 3.0 15.7 + - + +
396C LYS* 3.7 8.1 - - + +
397C ASN 3.1 0.4 - - - -
398C GLY* 1.3 77.2 - - - +
400C ASP* 1.3 74.0 + - - +
401C GLN 3.3 0.2 - - - -
402C THR* 3.3 2.9 + - - -
403C MET* 2.9 48.1 + - + +
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Residues in contact with ASP 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LYS* 2.8 52.5 + - - +
397C ASN* 4.4 2.7 - - - +
399C TYR* 1.3 89.5 - - - +
401C GLN* 1.3 55.8 + - - +
403C MET* 3.3 6.7 + - - +
404C GLN* 2.7 36.4 + - - +
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Residues in contact with GLN 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C PHE* 3.2 28.5 - - - -
320C ARG* 5.1 3.2 - - - +
321C VAL* 5.4 3.4 - - - +
372C ILE* 4.3 7.9 - - + +
373C TYR* 3.1 31.0 - - + +
374C ILE* 5.0 2.9 - - - -
397C ASN* 2.9 35.4 + - - +
398C GLY* 5.1 1.3 - - - -
400C ASP* 1.3 78.3 - - - +
402C THR* 1.3 64.0 + - - +
404C GLN* 3.5 33.2 + - - +
405C LEU* 3.3 21.3 + - - +
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Residues in contact with THR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET* 3.4 18.7 - - + +
56C ALA* 3.8 20.9 - - + -
57C LEU* 4.0 18.6 - - + -
372C ILE* 3.7 32.2 - - + +
374C ILE* 4.9 0.2 - - - +
398C GLY* 2.4 27.5 + - - -
399C TYR 3.3 3.5 + - - -
400C ASP 3.3 0.2 - - - -
401C GLN* 1.3 76.4 - - - +
403C MET* 1.3 60.7 + - - +
405C LEU* 3.4 2.3 + - - +
406C LEU* 2.9 34.8 + - + +
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Residues in contact with MET 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 3.5 24.0 - - - +
59C GLU* 3.5 30.7 - - - +
60C ARG* 3.3 49.1 - - + +
399C TYR* 2.9 38.1 + - + +
400C ASP* 3.6 7.2 - - - +
402C THR* 1.3 76.3 - - - +
404C GLN* 1.3 63.4 + - - +
406C LEU* 4.3 4.3 - - - -
407C ASP* 3.0 35.1 + - - +
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Residues in contact with GLN 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C VAL* 6.4 0.2 - - - +
325C LYS* 4.9 12.5 - - - +
400C ASP* 2.7 23.2 + - - +
401C GLN* 3.6 36.3 + - - +
402C THR 3.3 0.2 - - - -
403C MET* 1.3 74.8 - - - +
405C LEU* 1.3 59.6 + - + +
407C ASP* 4.0 6.2 + - - +
408C SER* 4.0 12.6 + - - -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C LEU* 4.6 2.5 - - + -
369C ASP* 3.3 44.9 - - - +
370C ASN* 4.3 6.1 - - - -
371C MET 3.2 34.5 - - - +
372C ILE* 3.8 22.2 - - + -
401C GLN 3.3 12.5 + - - +
402C THR 4.0 1.8 - - - +
403C MET 3.2 0.4 - - - -
404C GLN* 1.3 76.7 - - + +
406C LEU* 1.3 73.0 + - + +
407C ASP 3.2 1.8 - - - -
408C SER* 2.2 35.1 + - - +
409C HIS* 3.7 13.2 - - + +
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA 4.8 1.3 - - - +
57C LEU* 4.0 15.9 - - + -
60C ARG* 3.6 42.0 + - + +
62C LYS* 3.8 28.5 - - + -
307C LEU* 4.6 10.8 - - + -
372C ILE* 5.1 0.9 - - + -
402C THR* 2.9 30.5 + - + +
403C MET* 3.3 7.4 + - - +
405C LEU* 1.3 93.0 - - + +
407C ASP* 1.3 61.8 + - - +
408C SER 3.4 0.3 + - - -
409C HIS* 3.5 32.5 + - + +
410C LYS* 4.3 4.7 - - - +
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Residues in contact with ASP 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG* 2.6 43.8 + - - -
403C MET* 3.0 19.8 + - - +
404C GLN* 4.3 6.0 - - - +
405C LEU 3.2 0.2 - - - -
406C LEU* 1.3 74.8 - - - +
408C SER* 1.3 58.2 + - - +
409C HIS 3.2 1.3 - - - -
410C LYS* 3.2 34.2 + - + +
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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) + - + + + + + -
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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