Contacts of the helix formed by residues 345 - 353 (chain A) in PDB entry 3Q36
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 TYR 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A HIS* 3.2 19.6 + - - -
306A ARG* 3.2 46.4 + - - -
331A PHE* 3.6 15.9 - + - -
336A MET* 3.3 32.0 - - + +
340A LYS* 4.7 7.9 - - - -
341A PHE* 2.7 48.4 + + + +
342A ASP 4.1 0.2 + - - -
343A LYS 3.9 1.0 - - - -
344A GLY* 1.3 83.3 - - - +
346A SER* 1.3 54.0 + - - +
347A TYR 2.7 17.1 + - - +
348A ASN* 3.0 23.1 + - - +
349A ILE* 3.6 13.7 + - + +
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Residues in contact with SER 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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324A LEU* 4.0 17.7 - - - -
341A PHE* 3.2 11.7 + - - -
342A ASP* 2.6 44.2 + - - +
345A TYR* 1.3 75.7 - - - +
347A TYR* 1.3 60.6 + - - +
349A ILE* 3.7 13.1 - - - +
350A ARG* 3.0 33.5 + - - +
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Residues in contact with TYR 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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342A ASP 4.4 4.0 + - - +
343A LYS 6.1 1.8 - - - +
344A GLY 6.2 0.9 - - - -
345A TYR 2.7 7.7 + - - +
346A SER* 1.3 78.4 + - - +
348A ASN* 1.3 68.5 + - - +
350A ARG* 3.2 7.0 + - + +
351A HIS* 2.7 67.3 + + + +
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Residues in contact with ASN 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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303A HIS* 6.2 5.6 - - + -
306A ARG* 5.8 4.6 - - - +
307A MET* 6.0 5.6 - - + -
344A GLY 4.1 11.7 + - - -
345A TYR* 3.0 24.3 + - - +
347A TYR* 1.3 89.7 - - - +
349A ILE* 1.3 60.3 + - + +
351A HIS* 4.1 7.5 - - - +
352A SER* 2.6 35.6 + - - -
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Residues in contact with ILE 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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306A ARG* 6.1 4.0 - - - -
320A LEU* 3.6 13.9 - - + -
323A ALA* 4.1 16.2 - - + -
324A LEU* 3.5 28.7 - - + -
327A TRP* 4.3 29.2 - - + -
341A PHE* 4.4 13.9 - - + -
345A TYR* 3.6 27.4 - - + +
346A SER* 3.3 6.1 + - - +
347A TYR 3.2 0.4 - - - -
348A ASN* 1.3 78.0 - - + +
350A ARG* 1.3 66.0 + - - +
352A SER* 3.0 22.9 + - - -
353A PHE* 3.3 10.6 - - + -
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Residues in contact with ARG 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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320A LEU* 3.3 42.7 - - + +
324A LEU* 3.9 26.2 - - + +
346A SER* 3.0 23.0 + - - +
347A TYR* 3.6 7.4 - - + +
349A ILE* 1.3 80.7 - - - +
351A HIS* 1.3 62.4 + - - +
353A PHE* 3.1 16.3 + - - +
354A GLY* 4.0 3.1 + - - -
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Residues in contact with HIS 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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347A TYR* 2.7 53.8 + + + +
348A ASN* 4.1 8.5 - - - +
349A ILE 3.3 0.2 - - - -
350A ARG* 1.3 73.1 - - - +
352A SER* 1.3 62.0 + - - +
353A PHE 3.1 1.0 + - - -
354A GLY* 3.2 20.1 + - - +
362A TYR 4.7 1.7 + - - -
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Residues in contact with SER 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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307A MET* 4.3 13.9 - - - +
310A GLY 6.2 1.8 - - - -
311A LEU* 4.1 20.5 - - - +
314A LYS* 3.0 13.4 + - - -
348A ASN 2.6 20.4 + - - -
349A ILE* 3.0 14.9 + - - -
351A HIS* 1.3 78.5 - - - +
353A PHE* 1.3 65.0 + - - +
354A GLY 3.4 3.0 + - - +
362A TYR* 2.9 28.6 + - - +
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Residues in contact with PHE 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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310A GLY 5.3 4.3 - - - -
313A LEU* 5.8 0.4 - - + -
314A LYS* 3.9 37.5 - - + -
318A LEU* 3.1 27.4 - - + -
319A THR* 3.2 21.3 - - - -
320A LEU* 3.3 32.3 - - + -
323A ALA* 3.6 21.8 - - + -
349A ILE* 3.3 18.6 - - + -
350A ARG 3.1 11.2 + - - +
352A SER* 1.3 85.2 - - - +
354A GLY* 1.3 55.4 + - - +
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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