Contacts of the helix formed by residues 331 - 343 (chain A) in PDB entry 1JQP
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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLY 4.1 4.2 + - - -
330A CYS* 1.3 78.4 - - - +
332A GLU* 1.3 64.9 + - - +
333A ALA* 2.9 22.1 + - - +
334A LEU* 3.0 36.7 + - - +
335A MET* 3.1 25.6 + - - +
426A GLU* 4.4 5.8 - - - -
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Residues in contact with GLU 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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331A ASN* 1.3 72.4 - - - +
333A ALA* 1.3 59.5 + - + +
335A MET* 3.1 8.2 + - - +
336A LYS* 2.9 41.1 + - + +
396A ASP* 4.5 4.5 - - - +
398A TRP* 3.8 18.5 - - + -
418A ARG* 2.9 34.8 + - - +
419A GLY* 3.1 26.1 - - - +
426A GLU* 4.2 18.4 + - - +
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Residues in contact with ALA 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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206A LEU* 4.4 4.3 - - - +
331A ASN* 2.9 13.8 + - - +
332A GLU* 1.3 79.6 - - - +
334A LEU* 1.3 62.8 + - + +
336A LYS* 3.3 11.7 + - - +
337A LEU* 3.1 21.7 + - - +
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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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323A VAL* 3.6 15.7 - - + +
324A GLY* 3.8 18.2 - - - +
329A GLY 3.7 17.9 - - - +
331A ASN* 3.0 34.0 + - - +
333A ALA* 1.3 77.9 - - + +
335A MET* 1.3 57.4 + - - +
337A LEU* 3.4 19.0 + - + +
338A GLU* 2.9 30.7 + - - +
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Residues in contact with MET 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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323A VAL* 4.2 5.4 - - + -
330A CYS* 3.6 28.7 - - - -
331A ASN 3.1 15.9 + - - +
332A GLU 3.1 7.2 + - - +
334A LEU* 1.3 75.3 - - - +
336A LYS* 1.3 60.4 + - - +
339A LEU* 2.8 27.6 + - - +
345A MET* 3.2 13.8 - - - +
347A VAL* 4.0 11.4 - - + -
384A LEU* 3.6 27.6 - - + -
398A TRP* 3.8 23.3 - - + -
425A ILE* 3.7 20.2 - - + +
426A GLU* 3.6 24.0 - - + -
429A ALA* 3.9 11.0 - - + -
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Residues in contact with LYS 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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206A LEU* 3.8 20.3 + - + +
207A PRO 4.8 4.2 + - - -
208A GLU* 6.1 1.0 - - - +
332A GLU* 2.9 28.5 + - + +
333A ALA* 3.3 11.6 + - - +
335A MET* 1.3 75.8 - - - +
337A LEU* 1.3 62.0 + - - +
339A LEU* 3.4 3.1 + - - +
340A VAL* 3.1 31.4 + - - +
387A TYR* 3.9 41.3 - - + -
398A TRP* 3.8 15.3 - - + -
418A ARG* 3.9 21.3 - - - +
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Residues in contact with LEU 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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204A LEU* 4.2 13.9 - - + +
206A LEU* 3.7 28.4 - - + +
333A ALA 3.1 13.0 + - - +
334A LEU* 3.6 21.8 - - + +
335A MET 3.2 0.2 - - - -
336A LYS* 1.3 74.8 - - - +
338A GLU* 1.3 67.2 + - - +
339A LEU 3.3 0.2 + - - -
340A VAL* 4.0 0.5 - - - +
341A LYS* 2.9 52.9 + - + +
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Residues in contact with GLU 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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245A ARG* 2.8 28.8 + - - +
321A TYR* 2.9 36.2 + - - -
323A VAL* 4.2 11.6 - - + +
334A LEU 2.9 17.5 + - - +
335A MET 3.8 2.9 - - - +
337A LEU* 1.3 77.2 - - - +
339A LEU* 1.3 58.6 + - - +
341A LYS* 4.6 3.1 - - - -
342A HIS* 2.9 46.8 + - - +
343A GLY 3.5 4.2 + - - +
345A MET* 3.8 14.1 - - + -
431A ALA* 3.6 11.8 - - + +
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Residues in contact with LEU 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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210A TRP* 4.4 4.0 - - + -
212A TRP* 2.9 28.1 + - + +
335A MET 2.8 17.9 + - - +
336A LYS* 3.6 4.0 - - - +
337A LEU 3.2 0.2 - - - -
338A GLU* 1.3 76.5 - - - +
340A VAL* 1.3 58.3 + - - +
343A GLY 2.8 36.5 + - - +
344A PRO* 3.7 17.9 - - + -
345A MET* 3.3 13.0 - - + +
384A LEU* 3.9 20.9 - - + +
385A VAL 4.0 2.2 - - - +
386A GLY* 3.5 32.8 - - - +
387A TYR* 3.7 22.4 - - + -
398A TRP* 4.7 1.3 - - + -
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Residues in contact with VAL 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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204A LEU* 5.7 4.3 - - + -
206A LEU* 4.2 17.0 - - + -
207A PRO* 4.4 12.1 - - + -
210A TRP* 3.9 49.1 - - + +
212A TRP* 3.5 16.6 - - - -
336A LYS 3.1 17.3 + - - +
339A LEU* 1.3 75.3 - - - +
341A LYS* 1.3 62.5 + - - +
387A TYR* 3.6 25.6 - - + +
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Residues in contact with LYS 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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204A LEU* 4.7 16.4 - - + -
212A TRP* 5.3 1.3 - - - -
248A ILE* 6.1 1.0 - - - +
337A LEU* 2.9 45.6 + - + +
338A GLU* 5.8 0.2 - - - -
340A VAL* 1.3 80.2 - - - +
342A HIS* 1.3 91.4 + - + +
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Residues in contact with HIS 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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212A TRP* 4.8 1.3 - - - -
245A ARG* 3.1 31.6 + - - +
248A ILE* 4.5 8.5 - - - +
321A TYR* 4.0 5.6 + - - -
338A GLU* 2.9 47.9 + - - +
341A LYS* 1.3 109.1 + - + +
343A GLY* 1.3 59.8 + - - +
433A ILE* 4.4 17.7 - - + +
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Residues in contact with GLY 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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212A TRP* 3.3 14.3 - - - -
245A ARG* 3.0 11.8 + - - -
248A ILE* 3.9 4.0 - - - -
339A LEU* 2.8 32.7 + - - +
341A LYS 3.8 0.8 - - - -
342A HIS* 1.3 78.6 - - - +
344A PRO* 1.3 79.0 - - - +
345A MET* 3.6 0.7 + - - +
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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