Contacts of the helix formed by residues 337 - 345 (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 ASP 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A LYS 3.4 5.0 + - - -
336A MET* 1.3 73.6 - - - +
338A PRO* 1.3 74.2 - - - +
339A ASP* 2.7 38.7 + - - +
340A LYS* 2.8 36.2 + - + +
341A PHE* 3.1 8.5 + - - +
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Residues in contact with PRO 338 (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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328A LYS* 3.6 12.1 + - - +
332A ILE* 3.7 37.0 - - + -
336A MET 3.0 7.2 - - - +
337A ASP* 1.3 84.6 - - - +
339A ASP* 1.3 60.4 + - - +
341A PHE* 3.2 17.8 - - + +
342A ASP* 3.1 15.4 - - - +
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Residues in contact with ASP 339 (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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337A ASP* 2.7 19.0 + - - +
338A PRO* 1.3 72.9 - - - +
340A LYS* 1.3 62.7 + - - -
341A PHE 3.1 1.6 - - - -
342A ASP* 3.3 13.9 + - - +
343A LYS* 3.1 23.4 + - - +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A MET* 3.5 36.8 - - + -
337A ASP* 2.8 28.8 + - + +
339A ASP* 1.3 75.0 - - - +
341A PHE* 1.3 53.2 + - - +
343A LYS* 3.2 8.0 + - - +
344A GLY* 2.8 33.5 + - - -
345A TYR* 4.7 6.4 - - + -
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Residues in contact with PHE 341 (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* 4.4 9.0 - - + -
327A TRP* 3.9 22.9 - - + -
328A LYS* 3.2 50.9 - - + -
331A PHE* 4.0 18.8 - + + -
332A ILE* 5.5 2.2 - - + -
336A MET* 4.2 9.1 - - + -
337A ASP 3.1 6.2 + - - +
338A PRO* 3.2 12.8 - - + +
340A LYS* 1.3 80.3 - - - +
342A ASP* 1.3 68.7 + - - +
345A TYR* 2.7 72.1 + + + +
346A SER* 3.2 20.2 + - - -
349A ILE* 4.4 8.7 - - + -
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Residues in contact with ASP 342 (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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328A LYS* 2.9 26.6 + - - +
338A PRO 3.1 14.2 - - - +
339A ASP* 3.3 19.2 + - - +
341A PHE* 1.3 84.7 - - - +
343A LYS* 1.3 62.9 + - - +
344A GLY 3.5 0.3 + - - -
345A TYR 4.1 0.3 + - - -
346A SER* 2.6 31.5 + - - +
347A TYR* 4.4 4.3 + - - +
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Residues in contact with LYS 343 (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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339A ASP* 3.1 17.5 + - - +
340A LYS* 3.7 7.2 - - - +
342A ASP* 1.3 78.7 - - - +
344A GLY* 1.3 58.2 + - - +
347A TYR* 6.1 1.4 - - - +
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A LYS* 2.8 19.0 + - - -
343A LYS* 1.3 77.1 - - - +
345A TYR* 1.3 75.3 + - - +
347A TYR* 5.5 1.3 - - - -
348A ASN* 4.1 9.5 + - - -
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Residues in contact with TYR 345 (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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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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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