Contacts of the helix formed by residues 370 - 379 (chain A) in PDB entry 2PFP
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 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLY 4.9 0.5 + - - -
368A SER 5.8 0.2 - - - +
369A LEU* 1.3 76.5 - - - +
371A THR* 1.3 66.5 + - - +
372A GLN* 3.6 10.9 + - - +
373A GLN* 2.9 44.9 + - - +
374A ALA* 3.0 21.9 + - - +
11T G 5.2 16.6 - - - -
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Residues in contact with THR 371 (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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370A THR* 1.3 73.7 - - - +
372A GLN* 1.3 65.3 + - + +
374A ALA* 3.4 6.8 + - - +
375A ILE* 3.2 35.8 + - + +
460A ASP 5.2 3.4 - - - +
11T G 3.9 19.5 + - - -
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Residues in contact with GLN 372 (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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342A TRP* 3.5 33.8 - - + +
343A GLY* 4.4 10.5 - - - +
370A THR* 3.2 9.9 + - - +
371A THR* 1.3 81.6 - - + +
373A GLN* 1.3 56.7 + - - +
375A ILE* 3.1 7.1 + - - +
376A GLY 2.8 24.1 + - - -
460A ASP 5.6 0.4 - - - +
461A LEU* 2.9 41.7 + - - +
462A VAL* 3.4 17.2 - - - +
3P G 5.8 2.7 + - - +
4P T 6.1 0.9 - - - +
9T C 5.7 1.0 + - - -
10T T 3.8 26.2 + - - +
11T G 5.6 2.0 - - - +
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Residues in contact with GLN 373 (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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341A ILE* 3.5 9.4 - - + +
342A TRP 3.5 7.2 - - - -
343A GLY 3.0 35.1 + - - +
344A ALA* 3.8 10.7 - - + +
348A THR* 3.8 19.0 + - - +
352A TRP* 3.8 16.8 - - + -
368A SER 4.0 1.9 - - - +
369A LEU* 3.5 20.7 - - + +
370A THR* 2.9 44.5 + - - +
372A GLN* 1.3 75.1 - - - +
374A ALA* 1.3 58.1 + - - +
376A GLY 3.2 0.3 + - - -
377A LEU* 2.9 30.8 + - - +
4P T 5.4 0.4 - - - -
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Residues in contact with ALA 374 (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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369A LEU* 4.2 20.8 - - + +
370A THR 3.0 16.3 + - - +
371A THR* 3.7 7.4 - - - +
373A GLN* 1.3 75.2 - - - +
375A ILE* 1.3 63.3 + - + +
377A LEU* 3.9 3.5 - - - +
378A LYS* 3.1 24.1 + - - +
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Residues in contact with ILE 375 (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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371A THR* 3.2 27.1 + - + +
372A GLN 3.1 6.8 + - - +
374A ALA* 1.3 78.8 - - + +
376A GLY* 1.3 62.1 + - - +
378A LYS* 3.3 9.9 + - - +
379A HIS* 3.2 35.1 + - + -
383A PHE* 4.7 1.1 - - + -
459A ASP* 3.7 36.1 - - + +
460A ASP 3.3 27.1 - - - +
461A LEU* 3.6 20.6 - - + -
476A VAL* 4.2 4.7 - - + -
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Residues in contact with GLY 376 (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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341A ILE* 4.0 6.2 - - - -
342A TRP* 4.1 28.4 + - - -
372A GLN 2.8 14.2 + - - -
373A GLN 3.2 3.1 + - - -
375A ILE* 1.3 79.3 - - - +
377A LEU* 1.3 55.8 + - - +
379A HIS 3.3 2.9 + - - -
380A TYR* 2.9 28.4 + - - +
383A PHE* 4.2 9.4 - - - -
461A LEU* 4.9 0.2 - - - +
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Residues in contact with LEU 377 (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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341A ILE* 3.8 13.4 - - + +
360A LEU* 4.1 40.8 - - + +
363A ILE* 4.1 10.5 - - + -
364A ARG* 4.0 33.7 - - + +
369A LEU* 4.1 18.4 - - + -
373A GLN 2.9 17.0 + - - +
374A ALA* 3.9 4.7 - - - +
376A GLY* 1.3 73.8 - - - +
378A LYS* 1.3 66.6 + - - +
380A TYR* 3.1 20.9 + - + +
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Residues in contact with LYS 378 (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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374A ALA 3.1 15.8 + - - +
375A ILE* 3.6 10.9 - - - +
376A GLY 3.3 0.2 - - - -
377A LEU* 1.3 76.1 - - - +
379A HIS* 1.3 89.1 + - + +
380A TYR 3.5 0.2 - - - -
382A ASP* 5.5 0.2 - - - +
459A ASP* 2.5 29.3 + - - -
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Residues in contact with HIS 379 (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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375A ILE* 3.2 28.7 + - + +
376A GLY 3.3 3.6 - - - -
377A LEU 3.1 0.6 - - - -
378A LYS* 1.3 104.8 + - + +
380A TYR* 1.3 66.0 + - - +
381A SER 3.3 2.2 - - - -
382A ASP* 3.2 14.7 + - + -
383A PHE* 2.8 57.6 + + + -
459A ASP* 3.1 21.8 + - - -
476A VAL* 4.1 3.3 - - + +
486A HIS* 3.5 43.9 + + + +
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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