Contacts of the helix formed by residues 335 - 351 (chain G) in PDB entry 4HY0
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 GLY 335 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F ASN* 3.3 14.8 - - - -
330G LEU 3.6 2.0 + - - -
331G LEU* 2.8 29.5 + - - -
332G GLU 5.4 0.4 - - - -
333G GLN 3.8 0.2 - - - -
334G LYS* 1.3 74.7 - - - +
336G GLN* 1.3 68.0 + - - -
337G GLU 3.3 3.3 + - - -
338G TYR 3.3 3.1 + - - -
339G ILE* 3.2 21.6 + - - +
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Residues in contact with GLN 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ASN* 3.5 21.2 + - + +
256F LEU 4.4 6.2 - - - +
258F ARG* 5.1 0.9 - - - +
302F HIS* 2.9 57.5 + - - +
303F CYS* 3.5 8.8 - - - -
326F GLY* 3.7 25.2 + - - +
327F CYS* 4.1 2.5 - - - -
328F LYS* 3.3 20.6 - - - +
331G LEU* 3.5 7.3 - - - +
335G GLY* 1.3 68.0 - - - -
337G GLU* 1.3 76.6 + - - +
339G ILE* 3.2 5.2 + - - +
340G ASN* 3.0 38.2 + - - +
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Residues in contact with GLU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU* 3.8 22.2 - - + +
338A TYR* 3.6 35.5 - - + +
341A ASN* 4.2 7.9 - - + +
255F ASN* 5.5 0.9 - - - +
258F ARG* 2.9 42.1 + - - +
303F CYS 4.2 3.1 - - - +
335G GLY 3.4 1.4 - - - -
336G GLN* 1.3 92.4 - - - +
338G TYR* 1.3 57.1 + - - +
340G ASN* 3.7 3.4 + - - +
341G ASN* 2.8 38.6 + - - +
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Residues in contact with TYR 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU* 3.4 30.9 - - + +
258B ARG* 3.6 28.0 + - - -
315G ASP* 4.3 4.7 + - - -
317G TRP* 3.4 11.4 - - + +
318G GLU* 3.2 26.2 + - - +
321G ALA* 3.8 15.7 - - + -
330G LEU* 4.8 1.3 - - + -
334G LYS* 3.6 63.5 + - + +
335G GLY 3.3 3.0 + - - +
337G GLU* 1.3 76.7 - - - +
339G ILE* 1.3 66.6 + - + +
341G ASN* 3.6 1.4 - - - +
342G ILE* 3.1 44.7 + - + +
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Residues in contact with ILE 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325F PRO* 4.8 0.9 - - + -
326F GLY* 3.6 19.5 - - - +
321G ALA* 4.7 8.3 - - - +
325G PRO* 3.6 44.2 - - + +
330G LEU* 3.9 21.8 - - + -
331G LEU* 3.5 49.1 - - + +
335G GLY 3.2 9.6 + - - +
336G GLN 3.2 5.5 + - - +
337G GLU 3.2 0.6 - - - -
338G TYR* 1.3 84.6 - - + +
340G ASN* 1.3 61.5 + - - +
342G ILE* 3.5 2.1 + - - +
343G HIS* 3.1 22.2 + - - +
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Residues in contact with ASN 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASN* 3.9 15.6 - - - +
258F ARG* 6.1 0.8 - - - +
303F CYS* 4.0 27.1 + - - +
323F TRP 5.6 0.4 - - - +
324F TYR* 3.4 30.4 - - + +
325F PRO* 3.5 2.1 - - - +
326F GLY* 2.9 29.6 + - - -
327F CYS 4.2 1.8 - - - +
336G GLN* 3.0 23.7 + - - +
337G GLU* 4.0 2.9 + - - +
339G ILE* 1.3 75.0 - - - +
341G ASN* 1.3 63.0 + - - +
343G HIS* 3.4 5.9 + - - +
344G LEU* 3.1 30.6 + - + +
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Residues in contact with ASN 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU* 3.7 28.8 + - + +
340A ASN* 4.0 15.8 + - - +
341A ASN* 2.8 45.6 - - - +
344A LEU* 5.8 3.8 - - - +
258B ARG* 4.8 9.0 + - - +
337G GLU 2.8 20.8 + - - +
338G TYR 3.6 4.7 - - - +
339G ILE 3.2 0.2 - - - -
340G ASN* 1.3 70.3 - - - +
342G ILE* 1.3 61.5 + - - +
344G LEU* 3.0 10.8 + - - +
345G THR* 2.8 32.8 + - - +
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Residues in contact with ILE 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 3.5 23.3 - - - +
318G GLU* 3.7 32.3 - - + +
321G ALA* 3.9 4.5 - - + -
322G LYS* 3.7 35.2 - - + +
338G TYR* 3.1 58.0 + - + +
339G ILE 4.1 2.7 - - - +
341G ASN* 1.3 79.4 - - - +
343G HIS* 1.3 52.1 + - - +
345G THR* 3.3 8.3 + - - -
346G HIS* 2.7 33.1 + - - +
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Residues in contact with HIS 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F LYS 3.2 16.9 + - - -
323F TRP* 3.3 27.6 + + - -
325F PRO* 3.6 18.9 - - + +
343F HIS* 3.9 0.4 + - - -
346F HIS* 3.7 15.3 - + - -
402F ZN 2.7 30.7 - - - -
321G ALA 5.4 1.5 + - - +
325G PRO* 5.5 1.8 - - + -
339G ILE 3.1 17.7 + - - +
340G ASN* 3.6 7.0 - - - +
341G ASN 3.1 0.8 - - - -
342G ILE* 1.3 77.7 - - - +
344G LEU* 1.3 63.1 + - + +
346G HIS* 3.6 1.1 + - - +
347G SER* 3.0 36.9 + - - -
402G ZN 2.4 35.7 - - - -
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Residues in contact with LEU 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASN* 5.0 12.3 - - - +
344A LEU* 4.5 28.3 - - + -
345A THR* 4.8 12.8 - - - +
348A LEU* 6.2 3.6 - - + -
323F TRP* 4.3 19.5 - - + +
324F TYR* 4.9 11.4 - - + -
403F 1AQ 4.5 28.5 - - - -
340G ASN* 3.1 19.6 + - + +
341G ASN* 3.0 9.0 + - - +
343G HIS* 1.3 78.9 - - + +
345G THR* 1.3 64.9 + - - +
347G SER* 3.4 9.6 + - - +
348G LEU* 3.0 33.3 - - + +
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Residues in contact with THR 345 (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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258B ARG* 5.8 1.9 + - - -
299B LYS* 5.7 2.9 - - - +
306B GLY 6.3 0.4 - - - +
324B TYR* 5.6 3.1 + - - -
403B 1AQ 3.2 38.6 - - + +
318G GLU* 4.8 12.3 - - - +
322G LYS* 6.2 0.4 - - - +
341G ASN* 2.8 16.7 + - - +
342G ILE* 3.5 13.1 - - + +
344G LEU* 1.3 76.5 - - - +
346G HIS* 1.3 65.2 + - - +
348G LEU* 3.7 2.9 + - - -
349G GLU* 3.2 25.6 + - - +
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Residues in contact with HIS 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F HIS* 4.0 2.5 - + - -
346F HIS* 4.7 10.3 - + - -
347F SER* 4.0 13.6 + - - -
322G LYS* 3.7 44.9 - - + +
323G TRP* 4.0 18.7 - + - -
342G ILE 2.7 20.5 + - - +
343G HIS* 3.7 4.1 + - - +
345G THR* 1.3 72.9 - - - +
347G SER* 1.3 72.1 + - - +
348G LEU 3.3 0.9 + - - -
349G GLU* 3.3 11.9 + - - +
350G GLU* 3.1 52.9 + - + +
402G ZN 3.3 26.1 - - - -
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Residues in contact with SER 347 (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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323F TRP* 4.1 12.8 - - - -
346F HIS* 3.9 22.6 - - - -
403F 1AQ 5.1 7.0 - - - -
343G HIS* 3.0 29.5 + - - -
344G LEU* 3.6 11.3 - - - +
345G THR 3.3 0.6 - - - -
346G HIS* 1.3 82.9 + - - +
348G LEU* 1.3 61.9 + - - +
350G GLU* 3.8 4.0 - - - +
351G CYS* 3.1 27.0 + - - +
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Residues in contact with LEU 348 (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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344A LEU* 5.8 3.4 - - + -
348A LEU* 6.4 0.2 - - + -
403B 1AQ 3.4 71.9 - - + +
403F 1AQ 4.0 34.1 - - + -
344G LEU* 3.0 28.0 - - + +
345G THR* 4.4 3.6 - - - +
346G HIS 3.3 0.4 - - - -
347G SER* 1.3 74.2 - - - +
349G GLU* 1.3 65.7 + - - +
350G GLU 3.4 0.4 - - - -
351G CYS* 3.8 16.9 + - - -
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Residues in contact with GLU 349 (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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294B GLU* 4.0 8.1 - - - +
297B LYS* 3.6 28.1 + - - +
299B LYS* 5.9 0.3 + - - -
403B 1AQ 3.5 38.8 - - + +
318G GLU* 5.6 1.2 - - - +
322G LYS* 3.3 25.9 + - - +
345G THR* 3.2 23.6 + - - +
346G HIS* 3.3 4.4 + - - +
348G LEU* 1.3 77.5 - - - +
350G GLU* 1.3 61.3 + - - +
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Residues in contact with GLU 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F HIS* 5.1 3.3 + - - +
347F SER* 3.9 21.9 + - - +
323G TRP* 4.5 9.4 - - - -
346G HIS* 3.1 49.4 + - + +
347G SER* 3.8 5.0 - - - +
349G GLU* 1.3 81.7 - - - +
351G CYS* 1.3 76.3 + - + +
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Residues in contact with CYS 351 (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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347G SER 3.1 23.9 + - - +
348G LEU* 3.8 16.6 - - - -
349G GLU 3.6 1.2 - - - -
350G GLU* 1.3 90.6 - - + +
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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