Contacts of the helix formed by residues 335 - 346 (chain A) in PDB entry 3EQR
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 ASN 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A PHE* 4.9 0.9 - - - -
333A GLY 4.1 0.6 + - - -
334A LEU* 1.3 75.4 - - - +
336A GLY* 1.3 67.2 + - - +
337A SER* 3.1 11.2 + - - -
338A GLN* 2.8 47.2 + - - +
339A ILE* 3.0 23.2 + - - +
333B GLY 3.5 18.2 - - - +
334B LEU* 3.3 27.1 - - - +
338B GLN* 4.9 6.9 - - - +
342B LYS* 5.9 0.4 - - - +
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Residues in contact with GLY 336 (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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294A PHE* 3.6 45.7 - - - -
302A LEU* 4.5 3.6 - - - +
335A ASN* 1.3 75.5 - - - +
337A SER* 1.3 56.4 + - - +
339A ILE* 3.3 2.9 + - - +
340A LEU* 2.8 30.3 + - - +
332B ILE* 4.0 10.9 - - - +
333B GLY* 4.0 4.6 - - - -
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASN* 3.1 8.1 + - - -
336A GLY* 1.3 72.1 - - - +
338A GLN* 1.3 62.4 + - - +
340A LEU* 3.4 3.7 + - - +
341A HIS* 3.0 30.2 + - - +
331B TRP* 3.6 7.6 - - - -
332B ILE* 2.5 49.6 + - - +
334B LEU* 4.1 10.7 - - - +
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY 4.2 2.9 - - - +
334A LEU* 3.3 27.6 - - + +
335A ASN* 2.8 53.1 + - - +
337A SER* 1.3 73.0 - - - +
339A ILE* 1.3 60.9 + - - +
341A HIS* 3.5 5.1 + - - +
342A LYS* 3.0 38.5 + - - +
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Residues in contact with ILE 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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294A PHE* 4.1 23.3 - - + +
295A ALA* 3.9 23.1 - - + +
302A LEU* 4.3 8.7 - - + -
331A TRP* 3.8 42.4 - - + +
334A LEU* 3.8 29.4 - - + +
335A ASN 3.0 17.8 + - - +
336A GLY* 3.7 6.7 - - - +
338A GLN* 1.3 73.8 - - - +
340A LEU* 1.3 66.1 + - - +
342A LYS* 3.2 7.8 + - - +
343A ILE* 2.9 31.2 + - + +
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Residues in contact with LEU 340 (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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299A PRO* 4.0 6.7 - - + +
302A LEU* 3.8 33.8 - - + +
303A LYS* 3.7 25.6 - - + -
336A GLY 2.8 20.9 + - - +
337A SER* 3.7 5.8 - - - +
339A ILE* 1.3 72.6 - - - +
341A HIS* 1.3 58.8 + - - +
343A ILE* 4.2 1.3 - - - -
344A ASP* 2.9 53.7 + - + +
345A LYS* 6.2 2.9 - - + +
328B GLN* 3.7 26.2 - - - +
332B ILE* 4.6 16.8 - - + -
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Residues in contact with HIS 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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337A SER 3.0 18.7 + - - +
338A GLN* 3.8 6.3 - - - +
340A LEU* 1.3 77.6 - - - +
342A LYS* 1.3 63.6 + - - +
345A LYS* 2.9 56.9 + - + +
346A GLU* 3.1 40.2 + - + +
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Residues in contact with LYS 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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331A TRP* 3.9 14.1 - - + -
334A LEU* 3.5 40.8 - - + -
338A GLN* 3.0 22.4 + - - +
339A ILE* 3.2 5.4 + - - +
341A HIS* 1.3 80.2 - - + +
343A ILE* 1.3 65.1 + - + +
346A GLU* 3.3 24.0 + - - +
347A GLY 3.2 6.6 + - - -
348A GLU* 3.0 52.5 + - + +
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Residues in contact with ILE 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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297A CYS 3.7 23.1 - - - +
299A PRO* 3.8 24.7 - - + +
302A LEU* 3.9 18.6 - - + -
314A TRP* 3.8 15.7 - - + -
331A TRP* 3.6 37.5 - - + +
339A ILE* 2.9 26.4 + - + +
340A LEU* 3.9 5.8 - - - +
342A LYS* 1.3 73.7 - - - +
344A ASP* 1.3 62.4 + - + +
347A GLY* 4.0 4.8 - - - -
348A GLU 3.7 6.3 - - - +
349A ARG* 2.8 35.8 + - - +
370A HIS* 4.2 5.5 + - - -
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Residues in contact with ASP 344 (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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299A PRO* 4.0 5.7 - - + +
303A LYS* 2.9 42.5 + - - +
340A LEU* 2.9 31.4 + - + +
343A ILE* 1.3 80.5 - - - +
345A LYS* 1.3 81.4 + - + +
347A GLY* 4.5 1.8 + - - -
370A HIS* 2.9 32.3 + - - -
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Residues in contact with LYS 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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340A LEU* 4.9 3.5 - - + +
341A HIS* 2.9 51.6 + - + +
344A ASP* 1.3 96.9 + - - +
346A GLU* 1.3 60.8 + - - +
347A GLY 3.5 0.8 + - - -
328B GLN* 6.1 0.8 - - - +
351B PRO* 5.0 15.8 - - - +
352B ARG 6.2 0.2 - - - -
354B GLU* 5.5 12.1 - - - -
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Residues in contact with GLU 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 HIS* 3.1 38.5 + - + +
342A LYS* 3.3 36.1 + - - +
345A LYS* 1.3 77.7 - - + +
347A GLY* 1.3 64.0 + - - +
348A GLU* 3.2 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