Contacts of the helix formed by residues 348 - 361 (chain B) in PDB entry 2H51
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 VAL 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B TRP* 3.1 23.0 + - + +
342B HIS 6.1 0.2 - - - +
346B GLY 3.5 3.9 + - - -
347B SER* 1.3 71.4 - - - +
349B PHE* 1.3 60.1 + - - +
351B GLY* 3.5 1.0 + - - -
352B ARG* 2.9 60.5 + - - +
377B PHE* 3.7 10.3 - - + -
383B ARG 5.7 1.1 - - - +
385B GLN* 2.9 33.0 - - - +
1C PHQ 5.3 10.8 - - + -
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Residues in contact with PHE 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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281A ILE* 3.7 27.1 - - + -
282A ILE 3.8 13.5 - - - -
283A GLN* 3.5 16.1 + - - +
330B PHE* 3.6 57.7 - + - -
331B CYS 4.0 8.5 - - - -
332B SER* 3.6 27.4 - - - -
347B SER 3.4 0.2 - - - -
348B VAL* 1.3 80.5 - - - +
350B ILE* 1.3 64.1 + - + +
352B ARG* 3.4 1.0 + - - +
353B LEU* 2.8 41.8 + - + +
373B VAL* 4.4 5.6 - - + -
377B PHE* 3.9 8.7 - - + -
385B GLN* 3.9 8.7 - - - +
387B PRO* 3.9 13.9 - - + -
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Residues in contact with ILE 350 (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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185A ASP* 3.8 23.3 - - + +
189A MET* 3.7 22.1 - - + +
233A VAL* 4.8 0.7 - - + -
235A MET* 4.2 17.7 - - + -
281A ILE* 4.3 14.1 - - + -
283A GLN* 3.8 26.7 - - + -
347B SER* 3.3 23.5 + - - +
348B VAL 3.3 0.4 - - - -
349B PHE* 1.3 90.1 - - + +
351B GLY* 1.3 57.5 + - - +
353B LEU* 3.3 5.1 + - + +
354B ILE* 2.9 49.0 + - + +
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Residues in contact with GLY 351 (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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185A ASP* 5.2 0.2 + - - -
345B MET 6.1 0.4 - - - -
347B SER 3.0 15.4 + - - -
348B VAL* 3.9 1.3 - - - -
350B ILE* 1.3 76.9 - - - +
352B ARG* 1.3 60.2 + - - +
354B ILE* 3.5 10.0 + - - +
355B GLU* 3.1 36.0 + - - +
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Residues in contact with ARG 352 (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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348B VAL* 2.9 40.8 + - - +
349B PHE 3.7 3.4 - - - +
351B GLY* 1.3 74.0 - - - +
353B LEU* 1.3 63.2 + - - +
355B GLU* 3.4 16.2 + - - +
356B HIS* 2.7 44.9 + - + -
373B VAL* 4.5 3.8 - - + -
376B SER* 2.8 70.8 + - - +
377B PHE* 3.7 30.4 - - + -
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A MET* 4.1 16.6 - - + -
192A LEU* 5.5 0.2 - - + -
281A ILE* 3.7 45.5 - - + -
330B PHE* 4.2 9.4 - - + -
349B PHE* 2.8 34.6 + - + +
350B ILE* 3.6 4.9 - - + +
352B ARG* 1.3 73.0 - - - +
354B ILE* 1.3 57.5 + - - +
356B HIS* 3.3 2.1 + - - +
357B MET* 2.9 49.0 + - + +
369B ILE* 5.2 0.4 - - + -
370B PHE* 3.8 33.2 - - + -
373B VAL* 4.2 11.1 - - + +
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Residues in contact with ILE 354 (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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129A SER* 3.7 21.8 - - - +
131A GLY* 4.9 1.1 - - - -
184A VAL 5.5 0.7 - - - +
188A GLY* 3.6 35.0 - - - +
189A MET* 3.6 16.8 - - - +
192A LEU* 4.0 19.9 - - + +
350B ILE* 2.9 40.0 + - + +
351B GLY* 3.7 9.2 - - - +
353B LEU* 1.3 75.3 - - - +
355B GLU* 1.3 59.5 + - + +
357B MET* 3.3 1.4 + - - +
358B GLN* 2.8 54.8 + - + +
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Residues in contact with GLU 355 (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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351B GLY* 3.1 25.3 + - - +
352B ARG* 3.8 23.3 + - - +
353B LEU 3.3 0.2 - - - -
354B ILE* 1.3 77.6 - - + +
356B HIS* 1.3 65.1 + - + +
358B GLN* 3.5 18.9 + - - +
359B GLU* 3.2 24.8 + - - +
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Residues in contact with HIS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ARG* 2.7 41.3 + - + +
353B LEU 3.9 0.7 - - - +
355B GLU* 1.3 76.5 - - + +
357B MET* 1.3 57.3 + - - +
359B GLU* 3.3 0.6 + - - -
360B TYR* 2.7 59.2 + + + +
369B ILE* 4.0 9.5 - - + +
372B LYS* 3.7 37.4 + - + -
373B VAL* 3.6 23.4 - - + +
376B SER* 3.9 24.1 - - - -
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Residues in contact with MET 357 (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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133A VAL* 3.9 1.9 - - - +
192A LEU* 3.8 29.6 - - + -
196A LEU* 4.7 12.8 - - + -
231A PHE* 4.9 15.7 - - - -
353B LEU* 2.9 42.5 + - + +
354B ILE 3.6 3.6 - - - +
356B HIS* 1.3 73.3 - - - +
358B GLN* 1.3 65.2 + - - +
361B ALA* 3.0 34.8 + - + +
366B VAL* 4.8 8.5 - - + -
369B ILE* 3.2 45.7 - - + +
370B PHE* 4.5 11.9 - - + -
400B LEU* 5.3 3.8 - - + -
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Residues in contact with GLN 358 (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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129A SER* 4.0 6.3 + - - -
130A GLU* 5.2 0.9 + - - +
131A GLY* 3.4 9.3 + - - -
132A ASN* 3.1 40.0 + - - +
133A VAL* 3.6 10.3 - - - +
134A LYS* 2.8 32.1 + - - +
192A LEU* 4.1 13.0 - - + +
354B ILE* 2.8 32.8 + - + +
355B GLU* 3.6 29.1 - - - +
357B MET* 1.3 73.4 - - - +
359B GLU* 1.3 60.7 + - + +
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Residues in contact with GLU 359 (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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134A LYS* 3.2 39.1 + - - +
355B GLU 3.2 14.8 + - - +
356B HIS 3.9 2.0 - - - +
357B MET 3.2 0.2 - - - -
358B GLN* 1.3 81.6 - - - +
360B TYR* 1.3 99.1 + - + +
361B ALA 3.7 0.4 - - - -
362B CYS* 3.4 20.4 - - - -
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Residues in contact with TYR 360 (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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356B HIS* 2.7 49.6 + + + +
359B GLU* 1.3 106.2 + - + +
361B ALA* 1.3 60.6 + - - +
362B CYS* 3.0 5.1 + - - -
363B SER* 3.1 7.6 + - - -
364B CYS* 2.9 43.3 + - - +
369B ILE* 4.0 16.6 - - + -
372B LYS* 3.8 43.4 + - + -
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Residues in contact with ALA 361 (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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133A VAL* 4.0 15.0 - - + -
196A LEU* 4.2 13.2 - - + -
357B MET* 3.0 28.6 + - + +
359B GLU 3.7 0.4 - - - -
360B TYR* 1.3 76.3 - - - +
362B CYS* 1.3 61.3 + - - +
363B SER 3.5 0.2 + - - -
364B CYS 3.8 8.5 - - - +
369B ILE* 3.8 17.0 - - + +
399B TYR* 5.2 2.3 - - - -
400B LEU* 4.4 11.6 + - + -
401B PHE 4.3 4.9 + - - -
402B PRO* 3.4 18.4 - - + +
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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