Contacts of the helix formed by residues 395 - 408 (chain W) in PDB entry 5IY9
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 SER 395 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127W GLY* 6.0 4.7 - - - -
255W THR* 3.3 37.8 + - - -
258W ARG* 4.8 2.5 - - - +
259W CYS* 3.4 23.9 + - - +
262W ASN* 5.7 1.6 + - - +
394W PHE* 1.3 77.9 - - - +
396W PRO* 1.3 59.4 - - - +
398W THR* 3.2 8.0 + - - -
399W LEU* 2.8 36.0 + - - +
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Residues in contact with PRO 396 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259W CYS* 3.6 15.9 - - - -
262W ASN* 5.3 2.0 - - + +
330W LEU* 5.3 3.2 - - + +
334W ARG* 3.3 22.0 - - + +
337W LEU* 3.5 32.8 - - + -
394W PHE* 3.1 43.3 - - + -
395W SER* 1.3 96.0 - - - +
397W LEU* 1.3 54.9 + - - +
399W LEU* 4.0 2.3 - - + +
400W LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 397 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131W ASP* 5.7 5.2 - - - +
334W ARG* 3.5 16.1 - - - +
338W GLU* 4.2 19.5 - - - +
394W PHE* 3.7 25.8 - - + +
395W SER 3.2 0.2 - - - -
396W PRO* 1.3 78.4 - - - +
398W THR* 1.4 70.0 + - + +
400W LEU* 3.2 16.3 + - + +
401W ALA* 3.1 26.6 + - + +
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Residues in contact with THR 398 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255W THR* 4.8 5.7 - - - +
394W PHE 2.8 35.5 + - - +
395W SER* 3.2 13.3 + - - -
397W LEU* 1.4 79.4 - - + +
399W LEU* 1.3 54.7 + - - +
401W ALA* 4.3 4.5 - - - +
402W ASN* 3.2 29.5 + - - +
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Residues in contact with LEU 399 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251W LEU* 6.3 6.1 - - + -
256W LEU* 3.8 36.6 - - + -
259W CYS* 4.2 19.3 - - + -
263W LEU* 6.2 0.7 - - + -
282W ARG* 4.9 9.2 - - + -
285W TYR* 5.2 12.6 - - + -
330W LEU* 4.3 23.6 - - + -
395W SER* 2.8 22.4 + - - +
396W PRO 4.0 3.8 - - - +
398W THR* 1.3 71.3 + - - +
400W LEU* 1.3 64.8 + - - +
401W ALA 3.2 0.2 + - - -
402W ASN* 3.3 5.0 + - + +
403W PHE* 3.1 34.2 + - + +
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Residues in contact with LEU 400 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327W GLU* 4.2 21.6 - - + +
330W LEU* 4.0 18.0 - - + +
331W GLY* 3.7 25.6 - - - +
334W ARG* 3.4 42.0 - - + +
396W PRO 3.0 21.7 + - - +
397W LEU* 3.2 14.6 + - + +
399W LEU* 1.3 70.3 - - - +
401W ALA* 1.4 59.9 + - + +
403W PHE* 3.9 3.3 - - - +
404W ALA* 3.1 28.4 + - + +
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Residues in contact with ALA 401 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397W LEU* 3.1 18.7 + - + +
398W THR* 4.3 4.5 - - - +
400W LEU* 1.4 81.2 - - + +
402W ASN* 1.4 55.4 + - - +
403W PHE 3.2 1.8 - - - -
404W ALA* 3.4 6.4 - - - +
405W THR* 2.7 40.7 + - - +
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Residues in contact with ASN 402 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249W VAL* 5.1 5.7 - - - +
250W ASN* 4.0 14.1 + - - +
251W LEU* 3.2 45.1 - - + +
398W THR 3.2 21.3 + - - +
399W LEU* 3.3 7.3 + - + +
401W ALA* 1.4 73.4 - - - +
403W PHE* 1.4 55.8 + - - +
405W THR* 3.5 7.1 + - - -
406W LEU* 2.9 27.9 + - - +
435W PHE* 3.7 28.2 - - - -
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Residues in contact with PHE 403 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285W TYR* 3.0 61.7 - + + -
288W LEU* 5.8 3.4 - - + -
316W GLN* 5.6 3.8 - - - -
323W ILE* 4.7 11.7 - - + -
326W ALA* 5.0 1.8 - - + -
327W GLU* 4.2 27.4 - - + -
330W LEU* 3.7 21.8 - - + -
399W LEU* 3.1 23.2 + - + +
400W LEU 3.9 2.5 - - - +
402W ASN* 1.4 73.0 + - - +
404W ALA* 1.3 60.3 + - - +
406W LEU* 3.1 19.8 + - + +
407W VAL* 2.8 52.6 + - + +
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Residues in contact with ALA 404 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327W GLU* 4.0 22.7 - - - +
400W LEU* 3.1 22.4 + - + +
401W ALA* 3.2 7.6 + - - +
403W PHE* 1.3 73.3 - - - +
405W THR* 1.3 59.3 + - - +
407W VAL* 3.5 9.4 - - - +
408W SER* 2.6 41.2 + - - +
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Residues in contact with THR 405 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249W VAL* 6.3 1.3 - - + -
401W ALA* 2.7 25.7 + - - +
402W ASN* 3.8 6.9 - - - -
404W ALA* 1.3 73.2 - - - +
406W LEU* 1.3 59.7 + - - +
408W SER* 3.2 2.0 + - - -
409W THR* 2.9 46.1 + - - +
410W TYR* 4.0 15.3 - - + -
414W PHE* 5.2 4.5 - - + -
435W PHE* 3.9 26.5 - - + -
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Residues in contact with LEU 406 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288W LEU* 6.1 4.3 - - + -
308W PRO* 5.0 12.1 - - + -
309W VAL* 5.8 7.4 - - + -
312W ASP* 5.7 13.5 - - + +
402W ASN* 2.9 18.3 + - - +
403W PHE* 3.1 25.5 + - + +
405W THR* 1.3 76.1 - - - +
407W VAL* 1.4 65.7 + - + +
408W SER 3.8 4.5 - - - +
409W THR* 5.1 0.2 - - - -
416W ILE* 4.2 23.1 - - + -
435W PHE* 4.1 12.7 - - + -
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Residues in contact with VAL 407 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312W ASP* 6.1 0.9 - - - +
323W ILE* 3.7 31.9 - - + -
324W ARG* 6.5 0.4 - - - -
327W GLU* 4.4 19.5 - - + +
403W PHE* 2.8 44.3 + - + +
404W ALA* 3.5 14.8 - - - +
406W LEU* 1.4 73.5 - - + +
408W SER* 1.3 68.1 + - - +
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Residues in contact with SER 408 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327W GLU* 5.6 0.9 + - - -
404W ALA* 2.6 33.8 + - - +
405W THR* 3.2 4.2 + - - -
406W LEU 3.8 3.7 - - - +
407W VAL* 1.3 82.8 - - - +
409W THR* 1.3 75.0 + - - -
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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
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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