Contacts of the helix formed by residues 330 - 344 (chain A) in PDB entry 1EQR
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 THR 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A SER 4.3 4.2 + - - -
329A LEU* 1.3 75.4 - - - +
331A ARG* 1.3 65.9 + - + +
332A LYS* 3.4 11.3 + - + +
333A GLN* 3.4 23.4 + - - +
334A ILE* 2.7 38.3 + - - +
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Residues in contact with ARG 331 (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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330A THR* 1.3 78.0 - - + +
332A LYS* 1.3 65.7 + - - +
334A ILE* 3.3 9.4 + - + +
335A ASP* 2.5 49.0 + - - +
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Residues in contact with LYS 332 (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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330A THR* 4.2 11.8 + - + +
331A ARG* 1.3 80.7 - - - +
333A GLN* 1.3 97.2 + - - +
335A ASP* 3.5 7.1 + - - +
336A GLU* 3.2 28.1 + - + +
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Residues in contact with GLN 333 (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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329A LEU* 4.1 19.1 - - + -
330A THR* 3.2 31.0 + - - +
332A LYS* 1.3 101.7 + - - +
334A ILE* 1.3 64.0 + - - +
335A ASP 3.0 1.3 - - - -
336A GLU* 2.6 51.2 - - - +
337A TYR* 3.4 14.9 + - + +
417A LEU* 6.3 0.9 - - + -
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Residues in contact with ILE 334 (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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329A LEU* 3.8 19.3 - - + -
330A THR 2.7 25.2 + - - +
331A ARG* 3.9 9.0 - - + +
333A GLN* 1.3 73.6 - - - +
335A ASP* 1.3 60.2 + - - +
337A TYR* 3.6 12.5 - - - +
338A GLY* 3.0 22.3 + - - -
349A LEU* 4.6 5.5 - - - +
351A TYR* 3.9 42.8 - - + +
353A LYS* 4.3 11.9 - - - +
391A MET* 4.0 18.8 - - + -
393A PHE* 4.1 11.9 - - + -
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Residues in contact with ASP 335 (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 ARG* 2.5 47.7 + - - +
332A LYS* 3.7 6.9 + - - +
333A GLN 3.0 0.4 - - - -
334A ILE* 1.3 77.9 - - - +
336A GLU* 1.3 64.7 + - - +
337A TYR 3.2 0.9 - - - -
338A GLY* 3.1 2.9 + - - +
339A ASN* 2.4 39.0 + - - +
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Residues in contact with GLU 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 LYS* 3.2 16.4 + - + +
333A GLN* 2.6 51.2 + - - +
335A ASP* 1.3 74.7 - - - +
337A TYR* 1.3 83.9 + - + +
339A ASN* 2.9 10.1 + - - +
340A PHE* 2.5 38.1 + - - +
412A LYS* 5.3 11.1 - - - +
416A ASP* 3.7 8.8 - - - +
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Residues in contact with TYR 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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329A LEU* 3.2 34.5 - - + +
333A GLN* 3.5 19.8 - - + +
334A ILE* 3.6 5.2 - - - +
335A ASP 3.2 0.2 - - - -
336A GLU* 1.3 96.3 + - + +
338A GLY* 1.3 62.5 + - - +
340A PHE* 3.0 19.0 + - + +
341A VAL* 3.0 18.9 + - - +
349A LEU* 3.5 19.1 - - + -
393A PHE* 3.8 13.2 - + - -
409A LEU* 3.5 18.2 - - + -
412A LYS* 5.0 8.7 - - + -
413A VAL* 3.8 23.8 - - + +
416A ASP* 3.2 38.1 + - - +
417A LEU* 3.7 14.9 - - - +
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Residues in contact with GLY 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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334A ILE 3.0 16.4 + - - -
335A ASP* 3.1 5.8 + - - -
337A TYR* 1.3 75.8 - - - +
339A ASN* 1.3 57.4 + - - +
341A VAL* 3.1 21.1 - - - +
342A LYS* 3.7 3.3 + - - +
347A LYS 4.1 6.9 - - - +
348A GLY* 4.1 6.2 - - - +
349A LEU* 3.8 20.8 - - - +
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Residues in contact with ASN 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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335A ASP* 2.4 37.8 + - - +
336A GLU* 3.4 8.7 + - - +
338A GLY* 1.3 71.2 - - - +
340A PHE* 1.3 66.2 + - - +
342A LYS* 2.8 22.6 + - - +
343A ILE* 2.8 16.9 - - + +
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Residues in contact with PHE 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 GLU 2.5 18.5 + - - +
337A TYR* 3.0 12.3 + - - +
339A ASN* 1.3 72.4 - - - +
341A VAL* 1.3 64.7 + - + +
343A ILE* 2.9 35.1 + - + +
344A TYR* 3.5 35.4 - + - -
405A ALA 4.5 1.1 - - - -
408A ALA* 3.4 15.0 - - + -
409A LEU* 3.3 50.0 - - + -
412A LYS* 3.8 41.3 - - + +
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Residues in contact with VAL 341 (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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337A TYR 3.0 10.9 + - - +
338A GLY 3.1 16.6 - - - +
340A PHE* 1.3 77.0 - - + +
342A LYS* 1.3 60.7 + - - +
344A TYR* 3.1 12.1 + - - -
346A ALA* 3.1 33.8 + - + +
347A LYS 4.4 1.3 - - - +
348A GLY 3.0 28.7 - - - +
349A LEU* 3.5 21.8 - - + -
405A ALA* 3.7 17.1 - - + +
406A MET* 4.8 2.2 - - - -
409A LEU* 3.9 25.4 - - + -
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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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338A GLY 4.2 2.9 - - - +
339A ASN* 2.8 24.1 + - + +
341A VAL* 1.3 79.1 - - - +
343A ILE* 1.3 65.7 + - + +
345A GLY* 2.7 25.8 + - - -
346A ALA 3.4 19.1 - - - +
347A LYS 4.4 4.9 - - - +
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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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339A ASN* 2.8 31.6 - - + +
340A PHE* 2.9 25.4 + - + +
342A LYS* 1.3 85.6 - - + +
344A TYR* 1.3 75.1 + - + +
345A GLY 3.1 3.7 + - - -
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Residues in contact with TYR 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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340A PHE* 3.5 45.5 - + - -
341A VAL* 3.1 2.6 + - - -
342A LYS 3.1 1.0 - - - -
343A ILE* 1.3 89.5 - - + +
345A GLY* 1.3 61.2 + - - +
346A ALA 3.3 2.2 - - - -
401A ILE* 3.4 21.8 - - - +
404A ASP* 3.7 25.2 - - + +
405A ALA* 3.5 28.0 - - + +
408A ALA* 3.5 22.1 - - + +
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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
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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