Contacts of the helix formed by residues 387 - 409 (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 THR 387 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386G PRO* 1.3 76.6 - - - +
388G PRO* 1.3 67.5 - - + +
389G GLU* 3.0 13.5 + - - +
390G GLN* 2.5 54.1 + - - +
391G ARG* 2.8 12.5 + - - +
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Residues in contact with PRO 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G PRO 4.1 3.6 - - - +
387G THR* 1.3 86.5 - - - +
389G GLU* 1.3 61.7 + - + +
390G GLN 3.2 0.2 - - - -
391G ARG* 3.6 36.9 - - + +
392G ALA* 3.2 28.2 + - - +
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Residues in contact with GLU 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387G THR* 3.0 10.9 - - - +
388G PRO* 1.3 83.1 - - + +
390G GLN* 1.3 58.9 + - - +
392G ALA* 4.7 2.4 - - - +
393G ARG* 3.6 22.7 + - - +
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Residues in contact with GLN 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378G GLU* 3.2 48.6 + - + +
379G VAL* 3.3 22.8 - - + +
383G ASN* 3.3 15.9 + - - +
386G PRO* 3.3 21.2 - - + +
387G THR* 2.5 52.7 + - - +
389G GLU* 1.3 79.7 - - - +
391G ARG* 1.3 58.3 + - - +
392G ALA 3.4 0.4 - - - -
393G ARG* 3.6 11.4 - - + +
394G ALA* 3.2 17.7 + - - +
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Residues in contact with ARG 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 4.3 30.6 - - + +
96G GLU* 5.4 6.2 + - - +
99G ASP* 5.1 12.5 + - - -
379G VAL* 4.8 2.7 - - + -
386G PRO* 3.7 38.7 + - + +
387G THR 2.8 13.3 + - - +
388G PRO* 3.6 31.8 - - + +
390G GLN* 1.3 75.3 - - - +
392G ALA* 1.3 57.9 + - - +
393G ARG 3.0 4.5 - - - -
394G ALA* 3.0 22.1 + - - +
395G VAL* 3.2 17.9 + - - +
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Residues in contact with ALA 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388G PRO 3.2 17.4 + - - +
389G GLU* 4.9 3.4 - - - +
391G ARG* 1.3 78.3 - - - +
393G ARG* 1.3 60.1 + - - +
394G ALA 3.4 0.2 - - - -
395G VAL* 3.6 10.2 + - - +
396G LYS* 3.3 20.4 + - - +
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Residues in contact with ARG 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375G ASN* 4.6 9.7 - - - +
377G GLY* 5.7 4.4 - - - -
389G GLU 3.6 21.1 + - - +
390G GLN* 3.6 12.5 - - + +
392G ALA* 1.3 80.7 - - - +
394G ALA* 1.3 60.5 + - - +
395G VAL 3.2 0.9 - - - -
396G LYS* 3.4 32.0 + - - +
397G ASN* 2.4 69.6 + - - +
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Residues in contact with ALA 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 4.6 7.2 - - + +
49G SER* 4.0 33.6 - - - +
374G ILE* 4.9 0.7 - - - +
375G ASN 4.8 6.3 - - - +
376G THR 4.7 8.5 - - - +
379G VAL* 4.4 14.4 - - + -
390G GLN 3.2 13.8 + - - +
391G ARG* 3.0 11.9 + - - +
393G ARG* 1.3 76.8 - - - +
395G VAL* 1.3 61.5 + - - +
397G ASN* 4.1 9.3 - - - +
398G GLY 3.6 13.5 + - - -
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Residues in contact with VAL 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 4.0 24.9 - - + +
51G LEU* 3.7 22.0 - - + -
52G GLY* 3.7 23.2 - - - +
55G GLN* 4.2 8.3 - - - +
96G GLU* 5.6 3.8 - - + +
391G ARG 3.2 18.6 + - - +
392G ALA* 4.0 9.4 - - - +
393G ARG 3.2 0.8 - - - -
394G ALA* 1.3 78.8 - - - +
396G LYS* 1.3 62.5 + - - +
397G ASN 3.3 1.8 - - - -
398G GLY 4.0 0.9 - - - +
399G TYR* 3.1 24.0 + - + +
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Residues in contact with LYS 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G ALA 3.3 13.4 + - - +
393G ARG* 3.4 38.0 + - - +
395G VAL* 1.3 77.8 - - - +
397G ASN* 1.3 58.2 + - - +
399G TYR* 4.6 1.8 - - - -
400G ASP* 2.8 53.8 + - + +
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Residues in contact with ASN 397 (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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317G PHE* 5.2 2.6 - - + -
374G ILE* 4.8 1.8 - - + -
375G ASN* 3.6 48.1 - - + +
377G GLY* 5.5 0.7 + - - -
393G ARG* 2.4 52.6 + - - +
394G ALA* 4.2 3.5 - - - +
395G VAL 3.3 0.6 - - - -
396G LYS* 1.3 75.7 - - - +
398G GLY* 1.3 60.9 + - - +
400G ASP* 5.1 0.9 - - - -
401G GLN* 2.9 47.4 + - + +
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Residues in contact with GLY 398 (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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49G SER 4.0 8.5 - - - -
52G GLY* 4.4 0.7 - - - -
53G MET* 3.4 14.9 - - - -
374G ILE* 3.7 28.4 - - - +
394G ALA 3.6 9.0 + - - -
395G VAL 3.7 2.4 + - - -
396G LYS 3.5 0.2 - - - -
397G ASN* 1.3 78.6 - - - +
399G TYR* 1.3 54.7 + - - +
402G THR* 2.4 32.7 + - - -
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Residues in contact with TYR 399 (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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52G GLY* 3.6 21.2 - - - +
55G GLN* 4.3 15.5 - - + +
56G ALA* 4.0 21.2 - - + +
59G GLU* 2.7 36.5 + - - -
395G VAL* 3.1 19.4 + - + +
396G LYS* 4.0 2.9 - - - +
397G ASN 3.1 0.6 - - - -
398G GLY* 1.3 76.0 - - - +
400G ASP* 1.3 80.4 + - - +
402G THR* 3.2 3.8 + - - -
403G MET* 2.9 47.9 + - + +
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Residues in contact with ASP 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396G LYS* 2.8 49.9 + - + +
397G ASN* 4.6 1.1 - - - +
399G TYR* 1.3 92.0 - - - +
401G GLN* 1.3 59.9 + - - +
403G MET* 4.0 5.3 - - - +
404G GLN* 3.3 22.0 + - - +
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Residues in contact with GLN 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G PHE* 3.3 34.9 - - - -
320G ARG* 4.4 10.7 - - - +
321G VAL* 5.4 2.6 - - - +
372G ILE* 4.4 9.6 - - + +
373G TYR* 3.1 23.5 + - - +
374G ILE* 5.3 1.6 - - + -
375G ASN 5.9 0.2 - - - +
397G ASN* 2.9 27.6 + - + +
398G GLY* 4.8 1.6 - - - +
400G ASP* 1.3 76.1 - - - +
402G THR* 1.3 64.2 + - - +
404G GLN* 3.3 22.8 + - - +
405G LEU* 3.3 19.9 + - - +
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Residues in contact with THR 402 (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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53G MET* 3.5 22.8 - - + +
56G ALA* 3.7 19.5 - - + -
57G LEU* 4.2 7.2 - - + -
372G ILE* 3.7 35.3 - - + +
374G ILE* 4.8 0.2 - - - +
398G GLY* 2.4 27.8 + - - -
399G TYR 3.2 3.3 + - - -
401G GLN* 1.3 79.0 - - - +
403G MET* 1.3 60.8 + - - +
405G LEU* 3.1 4.2 + - - +
406G LEU* 3.0 34.8 + - + +
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Residues in contact with MET 403 (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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56G ALA* 3.5 33.4 - - - +
59G GLU* 3.5 35.7 - - + +
60G ARG* 3.5 52.0 - - + +
399G TYR* 2.9 30.5 + - + +
400G ASP* 4.2 7.4 - - - +
402G THR* 1.3 76.2 - - - +
404G GLN* 1.3 58.9 + - - +
406G LEU* 3.6 6.5 + - - +
407G ASP* 2.9 34.1 + - - +
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Residues in contact with GLN 404 (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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325G LYS* 4.8 13.9 - - - +
400G ASP 3.3 15.9 + - - +
401G GLN* 3.3 30.1 + - - +
402G THR 3.1 0.8 - - - -
403G MET* 1.3 79.0 - - - +
405G LEU* 1.3 62.5 + - - +
407G ASP* 3.4 9.3 + - - +
408G SER* 3.4 17.3 + - - -
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Residues in contact with LEU 405 (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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307G LEU* 4.3 8.1 - - + -
369G ASP* 3.2 43.7 - - - +
370G ASN* 4.4 1.8 - - - -
371G MET 3.1 31.9 - - - +
372G ILE* 3.6 24.2 - - + -
401G GLN 3.3 8.3 + - - +
402G THR 3.1 6.8 + - - +
404G GLN* 1.3 77.4 - - - +
406G LEU* 1.3 68.8 + - + +
407G ASP 3.1 2.0 - - - -
408G SER* 2.3 34.6 + - - +
409G HIS* 3.5 20.1 + - + -
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Residues in contact with LEU 406 (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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56G ALA 4.4 6.1 - - - +
57G LEU* 3.9 26.5 - - + -
60G ARG* 3.7 47.1 + - + +
62G LYS* 4.1 11.0 - - + -
307G LEU* 4.8 7.9 - - + -
372G ILE* 4.6 2.2 - - + -
402G THR* 3.0 33.7 + - + +
403G MET* 4.0 4.3 - - - +
405G LEU* 1.3 93.2 - - + +
407G ASP* 1.3 62.2 + - - +
408G SER 3.3 0.2 - - - -
409G HIS* 3.6 26.7 + - + +
410G LYS* 4.1 9.9 - - - +
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Residues in contact with ASP 407 (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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60G ARG* 3.1 31.0 + - - -
403G MET* 2.9 20.6 + - - +
404G GLN* 3.7 9.0 - - - +
405G LEU 3.1 0.8 - - - -
406G LEU* 1.3 74.0 - - - +
408G SER* 1.3 63.7 + - - +
409G HIS 3.1 2.8 + - - -
410G LYS* 3.4 26.3 + - - +
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Residues in contact with SER 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G TYR* 4.2 11.8 + - - -
369G ASP* 4.5 13.2 + - - +
404G GLN 3.4 9.1 + - - -
405G LEU* 2.3 36.3 + - - +
407G ASP* 1.3 77.0 - - - +
409G HIS* 1.3 67.3 + - - +
410G LYS 3.2 5.9 + - - +
411G GLN* 4.8 2.9 - - - +
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Residues in contact with HIS 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 4.8 3.1 - - - +
33G PRO* 3.6 31.2 - - + +
35G HIS* 3.6 19.5 - + - -
62G LYS* 5.9 1.8 - - - -
307G LEU* 4.0 4.9 - - + -
366G TYR* 4.4 9.1 + - - -
368G ILE* 3.5 18.8 - - + +
369G ASP* 3.1 26.0 + - + -
370G ASN* 3.1 21.0 + - - -
405G LEU* 3.9 27.3 + - + -
406G LEU* 3.6 20.4 - - + +
407G ASP 3.1 0.6 - - - -
408G SER* 1.3 81.1 + - - +
410G LYS* 1.3 64.3 + - + +
411G GLN* 3.6 13.5 + - - +
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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
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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