Contacts of the helix formed by residues 333 - 341 (chain A) in PDB entry 1EYN
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 MET 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ASN 5.5 3.6 - - - +
331A ARG 3.8 2.2 - - - -
332A PHE* 1.3 78.6 - - - +
334A HIS* 1.3 62.7 + - - +
335A VAL 3.1 0.6 + - - -
336A PRO* 3.4 27.9 - - + +
337A GLU* 4.0 11.4 - - - +
366A MET 5.2 0.3 - - - +
367A ALA* 4.9 14.1 - - + +
368A THR 6.0 1.6 - - - +
369A ASP* 6.3 2.7 - - + -
372A ALA* 5.6 2.6 - - + +
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Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLN* 3.1 29.0 + - - -
308A ALA* 3.5 26.5 - - + +
311A THR* 3.2 34.9 + - + +
331A ARG* 3.2 19.7 + - + -
332A PHE* 3.6 14.4 - + - -
333A MET* 1.3 78.2 + - - +
335A VAL* 1.3 66.7 + - - +
337A GLU* 3.3 7.1 + - - +
338A LEU* 3.0 36.3 + - + +
367A ALA* 5.1 2.7 - - - -
372A ALA* 3.8 31.4 - - + +
375A SER* 5.2 2.0 - - - -
376A LEU* 4.5 5.8 - - + +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 4.1 9.9 - - + -
315A LEU* 5.5 1.8 - - + -
332A PHE* 2.9 20.0 + - + +
334A HIS* 1.3 93.6 - - + +
336A PRO* 1.3 66.2 - - + +
338A LEU* 3.2 8.1 + - - +
339A ILE* 2.9 42.8 + - + +
345A ALA* 4.1 18.8 - - + +
347A ILE* 3.8 21.3 - - + -
352A VAL* 3.9 25.6 - - + -
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Residues in contact with PRO 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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332A PHE 3.4 9.9 - - - +
333A MET* 3.4 30.1 - - + +
335A VAL* 1.3 94.1 - - + +
337A GLU* 1.3 65.4 + - + +
339A ILE* 3.4 13.9 + - + +
340A ARG* 3.1 27.9 + - - +
347A ILE* 4.5 7.9 - - + -
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Residues in contact with GLU 337 (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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333A MET 4.0 12.6 - - - +
334A HIS 3.3 7.3 + - - +
335A VAL 3.2 0.6 - - - -
336A PRO* 1.3 79.1 - - + +
338A LEU* 1.3 66.1 + - - +
340A ARG* 3.1 41.8 + - - +
341A MET* 3.3 15.8 + - - +
365A VAL* 3.1 17.1 - - + +
366A MET* 2.8 46.1 + - - +
367A ALA* 5.4 0.2 - - + -
376A LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 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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308A ALA 5.2 0.2 - - - +
312A LEU* 4.0 26.5 - - + -
315A LEU* 3.7 31.2 - - + -
334A HIS* 3.0 43.6 + - + +
335A VAL* 3.8 3.8 - - - +
337A GLU* 1.3 71.7 - - - +
339A ILE* 1.3 60.4 + - - +
341A MET* 2.9 24.8 + - - +
342A GLY 3.3 0.5 + - - -
343A ALA* 3.0 19.9 + - + +
360A LEU* 4.6 4.6 - - + +
375A SER* 5.1 4.5 - - - +
376A LEU* 3.9 15.0 - - + -
379A ALA* 3.7 30.7 - - + -
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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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315A LEU* 6.1 0.2 - - + -
335A VAL* 2.9 35.2 + - + +
336A PRO* 3.6 12.8 - - + +
337A GLU 3.2 0.2 - - - -
338A LEU* 1.3 75.8 - - - +
340A ARG* 1.3 61.1 + - + +
342A GLY* 2.9 19.8 + - - -
343A ALA* 3.6 26.5 + - + +
345A ALA* 3.8 25.8 - - + +
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Residues in contact with ARG 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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336A PRO* 3.1 12.2 + - - +
337A GLU* 3.1 44.1 + - - +
339A ILE* 1.3 81.2 - - + +
341A MET* 1.3 57.7 + - - +
342A GLY 3.2 1.2 + - - -
361A SER* 4.4 3.8 + - - -
362A GLY 5.3 0.2 - - - +
363A ALA* 4.0 16.7 - - + +
364A GLN* 2.8 40.2 + - - +
365A VAL* 3.9 3.6 - - - +
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Residues in contact with MET 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 GLU 3.3 7.8 + - - +
338A LEU* 2.9 21.9 + - - +
340A ARG* 1.3 76.3 - - - +
342A GLY* 1.3 57.8 + - - +
360A LEU* 3.3 15.4 - - + +
361A SER* 2.7 50.1 + - - +
363A ALA* 3.8 15.9 - - + -
365A VAL* 4.1 21.1 - - + -
376A LEU* 4.7 2.5 - - - +
379A ALA* 3.8 33.9 - - + -
380A GLY 3.9 1.3 - - - +
383A ALA* 3.7 22.2 - - + -
387A THR* 3.5 27.1 - - + +
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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
------------------------------------------------------------
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