Contacts of the helix formed by residues 332 - 341 (chain A) in PDB entry 1DJ9
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 LEU 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ASN* 1.9 25.6 + - - +
329A SER* 2.7 19.6 + - - +
331A ALA* 1.3 85.8 - - + +
333A GLN* 1.3 62.3 - - - +
335A ALA* 1.6 55.4 - - + -
336A GLU* 1.2 78.1 - - + +
339A ARG* 3.2 12.1 - - - +
347A GLY 5.4 0.2 - - - +
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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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325A VAL* 5.4 0.2 - - - +
327A ASP 4.0 4.5 - - - +
328A ASN* 2.4 36.8 + - - +
332A LEU* 1.3 78.8 - - + +
334A LEU* 1.3 59.9 + - - +
335A ALA* 3.0 14.1 - - - +
336A GLU* 3.8 3.6 - - + +
337A LYS* 3.0 44.8 - - + +
360A LEU* 5.6 0.4 - - - -
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Residues in contact with LEU 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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311A PHE* 3.9 30.1 - - + -
333A GLN* 1.3 74.1 + - + +
335A ALA* 1.3 51.0 + - - +
336A GLU 3.1 3.4 - - - -
337A LYS* 3.0 23.2 + - + +
338A LEU* 2.9 46.9 + - + +
360A LEU* 4.3 14.8 - - + +
379A VAL 5.7 0.2 - - - +
380A LEU* 4.2 25.6 - - + +
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Residues in contact with ALA 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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328A ASN* 5.3 1.8 - - - +
331A ALA 4.8 0.9 - - - +
332A LEU* 1.6 43.7 - - + -
333A GLN 3.0 4.0 - - - +
334A LEU* 1.3 75.1 - - - +
336A GLU* 1.3 56.0 + - - +
339A ARG* 3.3 21.5 + - - +
345A VAL* 3.2 32.3 - - + +
346A THR* 4.9 0.9 - - - +
347A GLY* 4.8 5.6 - - - +
360A LEU* 3.8 22.6 - - + +
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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 LEU* 1.2 96.6 - - + +
333A GLN* 3.8 4.7 - - + +
334A LEU 3.1 1.0 - - - -
335A ALA* 1.3 73.4 - - - +
337A LYS* 1.3 67.1 + - + +
338A LEU 3.2 1.1 - - - -
339A ARG* 2.9 32.6 + - + +
340A GLN* 2.6 62.1 + - - +
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Residues in contact with LYS 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 GLN* 3.0 48.5 - - + +
334A LEU* 3.3 17.9 - - + +
336A GLU* 1.3 82.0 - - + +
338A LEU* 1.3 65.8 - - + +
340A GLN* 3.3 30.6 + - - +
341A GLN* 3.0 28.3 + - - +
379A VAL* 5.2 0.9 - - - -
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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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334A LEU* 2.9 37.9 + - + +
337A LYS* 1.3 76.4 - - + +
339A ARG* 1.3 57.7 + - - +
341A GLN 2.9 16.6 + - - -
342A GLY 3.1 0.3 + - - -
343A CYS* 2.9 38.1 + - + +
345A VAL* 3.6 32.5 - - + -
360A LEU* 3.7 20.2 - - + -
362A LEU* 5.4 0.4 - - + -
376A LEU* 4.8 6.3 - - + -
379A VAL* 3.3 33.2 - - + +
380A LEU* 4.5 14.8 - - + +
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Residues in contact with ARG 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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24A TYR* 4.0 12.9 - - - -
41A TYR* 3.2 26.4 - - + -
331A ALA 5.5 2.4 + - - -
332A LEU* 3.2 8.5 - - - +
335A ALA 3.3 11.2 + - - +
336A GLU* 2.9 46.5 + - + +
338A LEU* 1.3 75.2 - - - +
340A GLN* 1.3 66.7 + - - +
341A GLN 3.1 0.9 + - - -
342A GLY 3.2 5.4 + - - -
343A CYS 3.3 11.1 + - - +
344A TRP* 3.6 50.9 - - + -
345A VAL 3.4 24.7 + - - +
346A THR* 3.8 13.7 + - - +
347A GLY 5.5 0.8 - - - +
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Residues in contact with GLN 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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41A TYR* 5.4 0.2 - - - -
336A GLU* 2.6 56.2 + - - +
337A LYS* 3.4 25.7 + - - +
339A ARG* 1.3 74.1 - - - +
341A GLN* 1.3 61.6 + - + +
342A GLY 3.6 0.7 + - - -
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Residues in contact with GLN 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 LYS 3.0 17.2 + - - +
338A LEU 2.9 9.9 + - - +
340A GLN* 1.3 81.0 - - + +
342A GLY* 1.3 56.9 + - - +
343A CYS* 3.4 1.0 + - - -
375A ARG* 2.9 35.6 + - - +
379A VAL* 3.5 20.9 - - + +
382A GLY 3.4 8.1 + - - -
383A ASN* 2.6 38.3 + - - +
384A GLY* 3.3 17.2 + - - +
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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