Contacts of the helix formed by residues 340 - 349 (chain A) in PDB entry 1PG3
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 ALA 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A THR* 2.9 10.5 + - - +
339A PRO* 1.3 76.0 - - - +
341A ARG* 1.3 64.7 + - - +
342A MET 3.4 2.2 - - - -
343A CYS* 3.4 4.6 + - - +
344A GLN* 2.9 37.0 + - + +
370A LYS 3.3 18.7 + - - +
371A ALA 3.2 15.9 - - - +
373A GLU* 4.0 17.7 - - + +
375A THR* 4.5 1.6 - - + -
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.0 21.2 + - - +
99A GLY 3.0 25.1 + - - -
100A ASP* 2.9 21.8 + - - -
102A THR* 3.6 21.2 + - - +
330A PHE* 3.5 21.9 - - + -
333A VAL 4.0 8.5 - - - +
334A PRO 3.3 7.6 - - - +
336A TRP* 2.9 38.8 + - - +
337A PRO* 3.8 12.1 - - - +
338A THR* 2.9 18.7 + - - +
339A PRO 3.2 0.8 - - - -
340A ALA* 1.3 77.1 - - - +
342A MET* 1.3 65.8 + - - +
344A GLN* 3.0 23.6 + - - +
345A VAL* 3.0 34.3 + - + +
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Residues in contact with MET 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 3.3 30.2 - - + -
304A THR* 5.3 2.7 - - + -
330A PHE* 6.2 0.4 - - - -
334A PRO* 3.0 33.9 + - + +
339A PRO 5.2 0.9 - - - +
340A ALA 3.4 0.8 - - - -
341A ARG* 1.3 75.0 - - - +
343A CYS* 1.3 68.4 + - - +
346A VAL* 3.2 23.4 + - - +
354A LEU* 3.7 34.8 - - + -
356A THR* 4.7 17.0 - - + -
360A ALA* 5.8 1.3 - - - -
361A ILE* 6.1 1.3 - - + -
364A LEU* 3.7 28.3 - - + -
398A TYR* 4.8 5.2 - - + -
402A ILE* 3.9 28.0 - - + -
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Residues in contact with CYS 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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340A ALA 3.4 2.0 + - - +
341A ARG 3.2 0.4 - - - -
342A MET* 1.3 86.3 - - - +
344A GLN* 1.3 65.8 + - - +
346A VAL* 3.1 11.2 + - - +
347A ASP* 3.0 26.5 + - - +
364A LEU* 6.1 0.4 - - - -
371A ALA* 3.6 20.6 + - - +
372A ILE* 4.1 1.3 - - - -
375A THR* 3.4 26.7 - - + +
377A ARG* 3.7 26.5 - - + -
402A ILE* 3.9 24.9 - - - -
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Residues in contact with GLN 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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102A THR* 6.3 0.6 - - - -
337A PRO* 5.6 2.2 - - - +
338A THR* 4.1 8.2 + - - -
340A ALA* 2.9 35.8 + - - +
341A ARG* 3.4 31.6 - - - +
343A CYS* 1.3 75.6 - - - +
345A VAL* 1.3 57.9 + - + +
347A ASP* 3.3 5.9 + - - +
348A LYS* 2.8 30.4 + - - +
373A GLU 5.1 1.9 - - - +
375A THR* 3.8 15.5 - - + -
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Residues in contact with VAL 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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98A GLU* 3.9 23.1 - - + +
302A TRP* 3.4 33.9 - - + -
328A LEU* 4.0 17.7 - - + -
330A PHE* 4.4 6.1 - - + -
341A ARG* 3.0 38.1 + - + +
342A MET 3.5 7.4 - - - +
343A CYS 3.2 0.2 - - - -
344A GLN* 1.3 73.8 - - + +
346A VAL* 1.3 65.0 + - - +
348A LYS* 3.6 7.6 - - + +
349A HIS* 3.0 31.6 + - + +
351A VAL* 4.1 0.5 - - - +
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Residues in contact with VAL 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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302A TRP* 3.9 15.9 - - + -
342A MET* 3.2 16.4 - - + +
343A CYS* 3.1 16.5 + - + +
345A VAL* 1.3 77.4 - - - +
347A ASP* 1.3 63.9 + - - +
350A GLN* 2.9 9.7 + - - -
351A VAL* 2.9 39.3 + - + +
354A LEU* 4.5 17.9 - - + -
377A ARG* 4.5 6.7 - - + -
379A SER* 3.7 9.8 + - - +
380A LEU* 3.8 34.5 - - + -
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Residues in contact with ASP 347 (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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343A CYS 3.0 13.1 + - - +
344A GLN* 3.8 7.1 - - - +
346A VAL* 1.3 74.5 - - - +
348A LYS* 1.3 68.6 + - - +
349A HIS 3.3 0.3 + - - -
350A GLN* 3.0 25.6 + - - +
375A THR* 3.2 14.8 - - - +
376A ASP* 2.6 36.1 + - - +
377A ARG* 2.8 28.5 + - - -
379A SER* 5.0 1.8 + - - -
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Residues in contact with LYS 348 (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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98A GLU* 3.0 32.8 + - - +
102A THR* 2.7 40.5 + - - +
105A SER* 4.1 13.2 + - - -
344A GLN 2.8 18.8 + - - +
345A VAL* 3.3 7.8 + - - +
347A ASP* 1.3 79.4 - - - +
349A HIS* 1.3 75.8 + - + +
350A GLN* 3.9 1.9 + - - +
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Residues in contact with HIS 349 (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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96A ILE* 3.8 32.4 - - + +
98A GLU* 2.8 31.0 + - + +
105A SER* 4.6 7.0 - - - -
107A HIS* 4.1 22.1 + + - -
300A ILE* 3.5 15.3 - - + +
328A LEU* 3.8 30.7 - - + -
345A VAL* 3.0 21.2 + - + +
348A LYS* 1.3 99.9 + - + +
350A GLN* 1.3 72.3 + - - +
351A VAL* 3.2 3.7 + - + -
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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
------------------------------------------------------------
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