Contacts of the helix formed by residues 387 - 407 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E SER 3.7 2.0 + - - -
386E PRO* 1.3 72.8 - - - +
388E PRO* 1.3 76.9 - - - +
389E GLU* 3.1 33.2 + - + +
390E GLN* 3.1 45.2 + - + +
391E ARG* 3.2 7.3 - - - +
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Residues in contact with PRO 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.7 26.9 - - + +
23A THR 3.6 24.9 - - - +
24A GLU* 4.0 10.1 - - - +
26A GLY* 3.4 13.3 - - - +
386E PRO 3.8 3.6 - - - +
387E THR* 1.3 92.1 - - - +
389E GLU* 1.3 63.1 + - - +
391E ARG* 3.2 20.9 + - + +
392E ALA 3.2 10.6 + - - -
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Residues in contact with GLU 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.0 34.3 + - - +
26A GLY* 5.0 2.7 - - - -
28A TYR* 4.4 2.6 + - - -
440A GLU* 3.9 15.8 - - - +
387E THR* 3.2 31.2 + - + +
388E PRO* 1.3 82.0 - - - +
390E GLN* 1.3 57.7 + - + +
391E ARG 3.3 0.4 - - - -
392E ALA* 3.7 6.7 + - - +
393E ARG* 3.5 18.5 + - - +
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Residues in contact with GLN 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E GLU* 3.1 51.0 + - + +
379E VAL* 3.4 19.0 - - + +
383E ASN* 3.2 26.9 - - - +
386E PRO* 3.3 8.3 - - + +
387E THR* 3.1 44.6 - - + +
389E GLU* 1.3 75.5 - - - +
391E ARG* 1.3 61.8 + - - +
393E ARG* 3.9 14.1 - - + +
394E ALA 3.7 9.9 + - - -
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Residues in contact with ARG 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.0 40.2 + - - +
25A ALA* 4.1 7.3 - - - +
48E ILE* 3.3 49.2 - - + +
96E GLU* 3.0 30.1 + - - +
99E ASP* 3.4 21.8 + - - -
379E VAL* 4.9 4.5 - - - -
386E PRO* 3.8 31.0 + - + +
387E THR 3.2 17.5 - - - +
388E PRO* 3.2 9.1 + - + +
390E GLN* 1.3 76.6 - - - +
392E ALA* 1.3 59.9 + - - +
393E ARG 3.1 1.8 - - - -
394E ALA* 3.0 21.8 + - - +
395E VAL* 3.2 17.5 + - - +
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Residues in contact with ALA 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.4 21.2 + - - +
26A GLY* 3.9 14.6 - - - +
27A GLN* 5.9 0.9 - - + -
388E PRO 3.2 8.3 + - - +
389E GLU* 4.0 7.0 - - - +
390E GLN 3.5 0.2 - - - -
391E ARG* 1.3 79.9 - - - +
393E ARG* 1.3 57.3 + - - +
395E VAL* 3.7 9.5 + - - +
396E LYS* 3.2 23.4 + - - +
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Residues in contact with ARG 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E ASN* 5.0 6.7 - - - +
377E GLY* 4.5 16.4 - - - -
378E GLU* 4.0 25.7 + - - +
389E GLU 3.5 14.5 + - - +
390E GLN* 4.2 11.7 - - - +
391E ARG 3.1 0.8 - - - -
392E ALA* 1.3 77.4 - - - +
394E ALA* 1.3 60.2 + - - +
395E VAL 3.3 0.2 - - - -
396E LYS* 3.4 30.7 - - - +
397E ASN* 2.8 65.3 + - - +
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Residues in contact with ALA 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ILE* 4.2 15.9 - - + +
49E SER* 4.0 23.5 - - - +
374E ILE* 4.6 1.6 - - - +
375E ASN 4.8 3.8 - - - +
376E THR 4.8 4.5 - - - +
379E VAL* 4.3 14.4 - - + -
390E GLN 3.7 11.2 + - - +
391E ARG* 3.0 11.9 + - - +
393E ARG* 1.3 77.5 - - - +
395E VAL* 1.3 63.2 + - - +
397E ASN* 3.6 9.1 + - - +
398E GLY* 3.1 18.7 + - - -
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Residues in contact with VAL 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 5.3 8.1 - - + +
27A GLN* 6.3 0.2 - - - +
550A LYS* 3.7 28.7 - - - +
48E ILE* 4.0 20.4 - - + +
51E LEU* 3.8 26.2 - - + -
52E GLY* 3.4 22.6 - - - +
55E GLN* 4.3 0.2 - - - +
96E GLU* 5.4 0.9 - - - +
391E ARG 3.2 13.2 + - - +
392E ALA* 3.8 11.9 - - - +
394E ALA* 1.3 76.4 - - - +
396E LYS* 1.3 59.2 + - - +
398E GLY 3.4 0.7 + - - -
399E TYR* 2.9 26.7 + - - +
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Residues in contact with LYS 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ASP* 4.0 24.1 + - - +
550A LYS* 5.4 3.8 - - - +
392E ALA 3.2 14.9 + - - +
393E ARG* 3.4 32.2 - - - +
394E ALA 3.3 0.2 - - - -
395E VAL* 1.3 79.2 - - - +
397E ASN* 1.3 68.1 + - - +
399E TYR* 3.3 5.0 + - + +
400E ASP* 2.9 55.4 + - - +
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Residues in contact with ASN 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E ILE* 4.3 4.3 - - + +
375E ASN* 3.3 47.2 + - + +
377E GLY* 4.9 2.8 - - - +
393E ARG* 2.8 58.9 + - - +
394E ALA* 4.0 4.0 - - - +
396E LYS* 1.3 80.7 - - - +
398E GLY* 1.3 61.5 + - - +
400E ASP* 4.7 4.6 - - - +
401E GLN* 3.2 32.7 + - - +
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Residues in contact with GLY 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E SER 4.1 5.4 - - - -
52E GLY 3.8 6.5 - - - -
53E MET* 3.9 3.0 - - - -
374E ILE* 3.8 25.1 - - - +
394E ALA 3.1 15.0 + - - -
395E VAL 3.8 2.7 - - - -
396E LYS 3.2 0.2 - - - -
397E ASN* 1.3 75.2 - - - +
399E TYR* 1.3 62.0 + - - +
402E THR* 2.4 33.6 + - - -
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Residues in contact with TYR 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LYS* 3.6 64.1 - - + +
551A GLY* 3.8 3.3 + - - -
52E GLY* 3.4 12.7 + - - +
55E GLN* 4.0 6.7 - - + -
56E ALA* 3.6 30.5 - - + +
59E GLU* 2.5 33.5 + - - -
395E VAL 2.9 18.1 + - - +
396E LYS* 3.8 4.5 - - - +
398E GLY* 1.3 77.0 - - - +
400E ASP* 1.3 70.6 + - - +
402E THR* 4.0 1.2 - - - -
403E MET* 3.0 48.2 + - + +
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Residues in contact with ASP 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E LYS* 2.9 43.8 + - - +
397E ASN* 4.2 3.4 - - - +
399E TYR* 1.3 90.4 - - - +
401E GLN* 1.3 61.8 + - - +
403E MET* 3.2 6.9 + - - +
404E GLN* 2.7 35.7 + - - +
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Residues in contact with GLN 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E PHE* 4.0 24.0 - - + -
320E ARG* 5.9 1.5 - - - +
321E VAL* 5.9 2.2 - - - +
372E ILE* 4.0 7.3 - - + +
373E TYR* 3.1 30.0 + - + +
374E ILE* 5.0 1.8 - - + -
375E ASN 5.9 0.2 - - - +
397E ASN* 3.2 20.1 + - - +
398E GLY 4.8 0.7 - - - +
400E ASP* 1.3 84.8 - - - +
402E THR* 1.3 63.4 + - - +
404E GLN* 2.5 41.6 + - - +
405E LEU* 3.2 22.5 + - - +
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Residues in contact with THR 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E MET* 3.6 27.2 - - + +
56E ALA* 3.9 20.4 - - + -
57E LEU* 4.1 16.2 - - + -
372E ILE* 3.7 33.1 - - + +
374E ILE* 4.6 0.2 - - - +
398E GLY* 2.4 28.2 + - - -
399E TYR 4.0 2.5 - - - -
401E GLN* 1.3 75.9 - - - +
403E MET* 1.3 61.9 + - - +
405E LEU* 3.7 0.9 + - - +
406E LEU* 3.2 28.6 + - + +
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Residues in contact with MET 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 3.6 30.3 - - - +
59E GLU* 3.6 27.8 - - - +
60E ARG* 3.4 52.7 - - + +
399E TYR* 3.0 35.0 + - + +
400E ASP* 3.4 6.3 - - - +
402E THR* 1.3 77.7 - - - +
404E GLN* 1.3 62.8 + - - +
405E LEU 3.2 0.2 - - - -
406E LEU* 3.9 3.3 - - - +
407E ASP* 3.1 36.1 + - - +
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Residues in contact with GLN 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E LYS* 4.8 12.9 - - - +
400E ASP 2.7 19.9 + - - +
401E GLN* 2.5 39.7 + - - +
403E MET* 1.3 75.1 - - - +
405E LEU* 1.3 61.6 + - - +
407E ASP* 3.9 7.6 + - - +
408E SER* 3.8 14.9 + - - -
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Residues in contact with LEU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E LEU* 4.2 12.8 - - + -
369E ASP* 3.2 44.6 - - + +
370E ASN* 4.0 10.3 - - - -
371E MET 3.2 23.6 - - - +
372E ILE* 3.5 26.0 - - + -
401E GLN 3.2 14.9 + - - +
402E THR 4.0 2.9 - - - +
403E MET 3.2 0.4 - - - -
404E GLN* 1.3 77.1 - - - +
406E LEU* 1.3 65.6 + - + +
407E ASP 3.1 1.8 - - - -
408E SER* 2.4 34.8 + - - +
409E HIS* 3.7 5.3 + - + -
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Residues in contact with LEU 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA 4.7 2.9 - - - +
57E LEU* 4.1 22.7 - - + -
60E ARG* 3.6 44.9 + - + +
62E LYS* 4.2 12.1 - - + -
307E LEU* 4.6 11.7 - - + -
372E ILE* 4.9 0.7 - - + -
402E THR* 3.2 30.2 + - + +
403E MET* 3.4 6.5 + - - +
405E LEU* 1.3 93.7 - - + +
407E ASP* 1.3 62.0 + - - +
409E HIS* 3.2 35.9 + - + +
410E LYS* 4.0 9.4 - - - +
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Residues in contact with ASP 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ARG* 2.8 30.8 + - - -
403E MET* 3.1 22.7 + - - +
404E GLN* 4.1 7.7 - - - +
405E LEU 3.1 0.2 - - - -
406E LEU* 1.3 73.1 - - - +
408E SER* 1.3 56.2 + - - +
409E HIS 3.1 8.9 + - - -
410E LYS* 3.5 26.5 + - - +
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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) + - + + + + + -
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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