Contacts of the helix formed by residues 345 - 358 (chain A) in PDB entry 4HS2
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 HIS 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A ILE* 3.7 35.9 - - + +
310A ASP* 4.9 4.3 - - - -
341A MET* 2.8 23.4 + - + +
344A SER* 1.3 106.1 + - - +
346A PRO* 1.3 67.2 - - - +
347A HIS* 3.1 27.1 - + + -
348A LEU* 2.9 38.7 + - + +
349A VAL 3.6 2.9 + - - -
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Residues in contact with PRO 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A MET 3.7 1.1 - - - +
342A VAL 3.6 18.4 - - - +
343A VAL 3.6 11.2 - - - +
344A SER 3.5 7.4 - - - +
345A HIS* 1.3 87.0 - - - +
347A HIS* 1.3 65.0 + - - +
349A VAL* 3.1 11.7 + - + +
350A ALA* 3.1 20.1 + - - +
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Residues in contact with HIS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP* 3.4 24.7 + - - -
344A SER 5.4 0.2 - - - -
345A HIS* 3.1 37.5 + + + -
346A PRO* 1.3 80.7 - - - +
348A LEU* 1.3 71.9 + - + +
350A ALA* 3.3 10.5 + - - +
351A GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 4.1 17.8 - - + +
307A ILE* 3.7 35.2 - - + +
310A ASP* 3.7 34.3 - - + +
318A LYS* 3.9 15.5 - - - -
341A MET* 4.0 13.2 - - - -
345A HIS* 2.9 33.1 + - + +
347A HIS* 1.3 90.6 - - + +
349A VAL* 1.3 64.2 + - - +
351A GLU* 3.3 10.0 + - + +
352A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TRP* 3.9 24.0 - - + -
341A MET* 3.8 21.8 - - + -
342A VAL* 3.8 40.2 - - + +
345A HIS 3.6 3.5 + - - +
346A PRO* 3.1 11.5 + - + +
348A LEU* 1.3 78.3 - - - +
350A ALA* 1.3 57.7 + - - +
352A ALA* 3.2 3.6 + - - +
353A TYR* 2.9 30.5 + - + +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PRO 3.1 11.9 + - - +
347A HIS* 3.4 13.5 - - - +
348A LEU 3.2 0.2 - - - -
349A VAL* 1.3 76.8 - - - +
351A GLU* 1.3 56.0 + - - +
353A TYR* 3.3 9.9 + - - +
354A ARG* 2.9 28.8 + - - +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LYS* 2.9 47.3 + - - +
322A VAL* 4.6 13.2 - - + +
347A HIS* 2.9 18.3 + - - +
348A LEU* 3.7 14.2 - - + +
349A VAL 3.3 0.2 - - - -
350A ALA* 1.3 74.3 - - - +
352A ALA* 1.3 64.0 + - - +
354A ARG* 3.3 11.1 + - + +
355A SER* 3.1 22.0 + - - -
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 5.0 4.5 - - + -
322A VAL* 4.0 20.8 - - + +
325A ILE* 5.0 7.6 - - + -
326A ASN* 3.6 13.8 - - - +
338A TRP* 4.9 15.7 - - + -
348A LEU 3.0 13.3 + - - +
349A VAL* 3.6 9.9 - - - +
351A GLU* 1.3 76.9 - - - +
353A TYR* 1.3 57.6 + - - +
355A SER* 3.2 3.6 + - - -
356A LEU* 2.9 30.8 + - - +
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Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A VAL* 2.9 16.4 + - + +
350A ALA* 3.4 13.2 - - - +
351A GLU 3.3 0.2 - - - -
352A ALA* 1.3 77.2 - - - +
354A ARG* 1.3 61.2 + - - +
356A LEU* 3.2 12.4 + - + +
357A ALA* 2.9 44.8 + - + +
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Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA 2.9 17.1 + - - +
351A GLU* 3.6 10.7 - - - +
352A ALA 3.3 0.2 - - - -
353A TYR* 1.3 82.3 - - + +
355A SER* 1.3 61.4 + - - +
357A ALA* 3.5 5.0 + - - +
358A SER* 3.1 24.4 + - - +
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A VAL* 3.6 22.2 - - - +
323A ASP* 4.1 9.4 + - - -
326A ASN* 3.3 11.0 + - - -
351A GLU* 3.1 9.9 + - - -
352A ALA 3.5 7.6 - - - -
354A ARG* 1.3 77.3 - - - +
356A LEU* 1.3 64.0 + - - +
358A SER* 3.0 21.6 + - - -
359A ALA* 3.3 10.2 + - - +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ASN* 3.5 39.5 - - + +
329A ALA* 5.7 7.0 - - + -
352A ALA 2.9 17.2 + - - +
353A TYR* 3.8 12.1 - - + +
355A SER* 1.3 75.1 - - - +
357A ALA* 1.3 61.8 + - - +
359A ALA* 3.3 27.4 + - + +
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A TYR* 2.9 37.6 + - + +
354A ARG* 3.7 6.1 - - - +
356A LEU* 1.3 77.8 - - - +
358A SER* 1.3 57.5 + - - +
359A ALA 3.2 5.9 + - - +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 3.1 16.1 + - - -
355A SER* 3.0 16.5 + - - -
357A ALA* 1.3 75.5 - - - +
359A ALA* 1.3 61.3 + - - +
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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