Contacts of the helix formed by residues 338 - 349 (chain B) in PDB entry 5H2U
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 LYS 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B ARG 4.5 0.6 + - - -
224B ASP* 2.8 40.2 + - - +
225B ASN* 2.9 14.8 + - - +
226B LEU 3.4 21.9 + - - +
227B LEU* 4.6 11.2 - - + +
336B LEU 4.0 0.8 + - - -
337B ILE* 1.3 72.8 - - - +
339B GLU* 1.3 67.0 + - - +
340B ASP* 3.4 2.7 - - + +
341B VAL* 3.0 31.6 + - + +
342B TYR* 3.1 11.6 + - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 5.8 1.0 - - - +
337B ILE 3.4 2.4 + - - -
338B LYS* 1.3 70.2 - - - +
340B ASP* 1.3 58.7 + - - +
342B TYR* 3.2 3.5 + - - +
343B LEU* 2.9 52.9 + - + +
503B GOL 4.0 38.7 + - - +
392C SER* 3.4 23.9 + - - +
394C HIS* 3.6 25.2 - - + +
395C GLU* 3.9 7.8 + - - +
398C LEU* 5.6 0.6 - - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B LYS* 3.4 2.3 - - + +
339B GLU* 1.3 80.0 - - - +
341B VAL* 1.3 55.0 + - + +
343B LEU* 4.6 4.2 - - - +
344B SER* 2.7 38.1 + - - -
347C HIS* 3.6 29.9 - - + +
348C ASN* 5.2 3.8 + - - +
392C SER* 3.3 14.0 - - - -
393C ASN* 2.7 34.5 + - - +
394C HIS* 3.2 30.0 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TYR* 3.9 17.1 - - + +
224B ASP 5.1 0.4 - - - +
225B ASN* 3.8 26.7 - - - +
337B ILE* 3.7 17.0 - - + -
338B LYS* 3.0 30.8 + - + +
340B ASP* 1.3 79.0 - - + +
342B TYR* 1.3 66.9 + - - +
344B SER* 3.7 4.4 + - - -
345B HIS* 3.5 18.7 + - - +
347C HIS* 4.1 28.8 + - + +
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Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TYR* 3.5 42.2 - + + -
311B ARG 3.2 21.6 + - - -
312B ASP* 2.7 39.9 + - + -
334B ALA* 3.8 14.1 - - + +
337B ILE* 4.1 1.1 - - + +
338B LYS 3.1 11.4 + - - +
339B GLU 3.8 4.5 - - - +
341B VAL* 1.3 77.6 - - - +
343B LEU* 1.3 85.8 + - + +
345B HIS* 2.9 32.2 + - - -
350B PRO* 3.5 17.9 - - + +
353B TRP* 6.0 1.2 - - - +
354B THR* 4.6 5.3 + - - -
364B TYR* 4.6 3.8 - - - -
502B GOL 3.7 9.8 + - - -
503B GOL 4.0 21.1 - - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 2.9 43.4 + - + +
340B ASP* 4.6 2.0 - - - +
342B TYR* 1.3 91.0 - - + +
344B SER* 1.3 60.1 - - - +
348B ASN* 3.1 21.1 - - - +
350B PRO* 3.6 14.3 - - + +
351B TYR* 3.7 16.1 - - + +
354B THR* 5.4 0.7 - - - +
359B LEU* 4.4 19.7 - - + -
364B TYR* 3.6 25.1 - - + +
503B GOL 5.3 3.4 - - - +
348C ASN* 4.1 9.2 - - - +
394C HIS* 3.8 33.4 - - + +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ASP 2.7 22.1 + - - -
341B VAL 3.7 2.6 + - - -
343B LEU* 1.3 76.7 - - - +
345B HIS* 1.3 66.5 + - - +
346B ASP 3.5 0.3 + - - -
347B HIS* 3.3 6.6 + - - -
348B ASN* 3.1 20.0 + - - -
344C SER* 4.0 10.0 + - - +
347C HIS* 3.2 32.5 + - - -
348C ASN* 3.3 18.6 - - - -
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TYR* 3.3 49.5 + + + +
316B ARG* 6.0 0.4 - - - -
341B VAL 3.5 6.6 + - - +
342B TYR* 2.9 29.7 + + - +
343B LEU 3.4 0.4 - - - -
344B SER* 1.3 78.2 + - - +
346B ASP* 1.3 86.7 + - - +
349B ILE* 3.2 40.7 + - + +
350B PRO* 3.5 12.1 - - + +
502B GOL 2.9 34.2 + - - -
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Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLY* 5.7 2.3 - - - -
201B TYR* 5.3 3.5 + - - -
344B SER 3.5 0.4 + - - -
345B HIS* 1.3 96.8 + - - +
347B HIS* 1.3 75.3 + - + +
349B ILE* 3.4 23.9 + - + +
393B ASN* 3.8 3.1 + - - -
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Residues in contact with HIS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B SER 3.3 3.0 + - - -
345B HIS 3.2 0.6 - - - -
346B ASP* 1.3 81.6 - - + +
348B ASN* 1.3 62.6 + - - +
393B ASN* 2.6 26.2 + - - +
225C ASN* 5.3 2.5 + - - -
340C ASP* 3.4 27.4 - - + +
341C VAL* 3.9 35.9 + - + +
344C SER* 3.2 24.7 + - - -
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LEU 3.1 13.8 - - - +
344B SER* 3.1 24.3 + - - -
345B HIS 3.2 0.6 + - - -
347B HIS* 1.3 77.0 + - - +
349B ILE* 1.3 58.5 + - - +
350B PRO* 3.1 3.8 - - - -
351B TYR* 2.9 51.2 + - + +
393B ASN* 3.4 9.6 - - + +
394B HIS* 5.7 2.7 - - + +
340C ASP* 4.4 6.3 + - - +
343C LEU* 4.1 7.7 - - - +
344C SER* 3.3 19.6 - - - +
348C ASN* 2.9 32.3 + - - +
351C TYR* 4.2 6.9 + - - -
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ARG* 5.9 0.9 - - - +
345B HIS* 3.2 45.0 + - + +
346B ASP* 3.4 19.0 + - + +
348B ASN* 1.3 76.1 - - - +
350B PRO* 1.4 65.2 - - + +
351B TYR 3.1 1.4 + - - -
352B LYS* 3.3 15.4 + - + +
353B TRP* 3.3 34.3 - - + -
386B VAL* 4.5 11.0 - - + -
393B ASN* 3.3 24.4 - - - +
502B GOL 4.1 10.5 - - - -
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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
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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