Contacts of the helix formed by residues 463 - 476 (chain A) in PDB entry 1P3F
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 ARG 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A LEU 3.9 0.8 + - - +
462A ILE* 1.3 76.9 - - - +
464A LYS* 1.3 58.9 + - - +
466A PRO* 2.7 38.7 - - + +
467A PHE* 3.1 12.2 + - - +
23B ARG* 4.3 8.1 - - - +
30B THR* 3.6 27.3 + - - +
33B ALA* 5.1 1.8 - - - +
36B ARG* 4.9 3.8 - - - +
59I G 4.1 9.1 + - - -
60I C 3.2 49.5 + - - +
236J T 4.3 7.1 + - - -
237J T 3.1 50.2 + - - +
238J T 3.7 15.3 - - - +
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Residues in contact with LYS 464 (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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460A LEU* 5.0 3.6 - - + -
462A ILE 3.4 3.4 + - - +
463A ARG* 1.3 70.5 - - - +
465A LEU* 1.3 54.1 + - - +
467A PHE* 2.8 5.9 + - - +
468A GLN* 2.6 37.4 + - + +
490A MET* 3.0 48.0 - - - +
493A GLN* 4.1 15.9 - - - +
238J T 3.4 17.5 + - - +
239J T 6.1 0.9 - - - +
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Residues in contact with LEU 465 (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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464A LYS* 1.3 77.0 - - + +
466A PRO* 1.3 70.4 - - + +
468A GLN* 2.9 19.6 + - + +
469A ARG* 2.7 51.3 + - + +
237J T 3.8 24.0 - - + +
238J T 3.0 42.6 + - + +
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Residues in contact with PRO 466 (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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462A ILE* 5.7 0.9 - - + -
463A ARG* 2.7 45.3 - - + +
465A LEU* 1.3 88.6 - - + +
467A PHE* 1.3 61.0 + - - +
469A ARG* 3.0 27.0 + - - +
470A LEU* 2.8 22.7 + - - +
25B ASN 4.7 3.4 - - - +
28B GLY* 3.5 29.8 - - - +
29B ILE* 4.9 4.0 - - + -
237J T 3.5 22.0 - - - +
238J T 4.1 2.2 - - - +
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Residues in contact with PHE 467 (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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462A ILE* 4.2 25.8 - - + -
463A ARG 3.1 9.4 + - - +
464A LYS 2.8 10.4 + - - +
466A PRO* 1.3 77.8 - - - +
468A GLN* 1.3 67.8 + - - +
470A LEU* 2.9 7.5 + - + +
471A VAL* 2.9 39.6 + - + +
489A VAL* 4.0 13.5 - - + -
492A LEU* 4.2 1.3 - - + -
493A GLN* 3.3 60.3 - - + +
496A SER* 3.7 20.9 - - - -
29B ILE* 4.5 10.9 - - + +
58B LEU* 4.9 3.1 - - + -
62B LEU* 4.0 23.6 - - + -
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Residues in contact with GLN 468 (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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464A LYS 2.6 17.1 + - - +
465A LEU* 3.5 24.2 - - + +
467A PHE* 1.3 73.1 - - - +
469A ARG* 1.3 57.7 + - - +
471A VAL* 3.4 2.2 + - - +
472A ARG* 2.9 65.0 + - + +
484A PHE 5.5 0.6 + - - -
486A SER* 5.3 6.9 - - - +
489A VAL* 3.8 39.7 - - + +
51I A 5.1 0.8 + - - -
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 2.7 37.0 + - + +
466A PRO* 3.0 26.5 - - - +
468A GLN* 1.3 78.3 - - - +
470A LEU* 1.3 56.8 + - - +
472A ARG* 3.2 7.1 + - - +
473A GLU* 2.9 30.3 + - - +
23B ARG* 4.5 17.0 - - - +
25B ASN* 3.0 30.8 + - - +
28B GLY* 5.1 1.0 - - - -
237J T 2.9 43.4 + - - -
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Residues in contact with LEU 470 (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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466A PRO 2.8 15.0 + - - +
467A PHE* 2.9 10.3 + - + +
469A ARG* 1.3 70.3 - - - +
471A VAL* 1.3 68.0 + - - +
473A GLU* 3.3 8.6 + - - +
474A ILE* 3.0 44.3 + - + +
25B ASN* 4.2 13.2 - - + +
26B ILE* 3.7 43.5 - - + +
29B ILE* 3.7 25.4 - - + -
58B LEU* 3.8 4.9 - - + -
59B LYS* 5.8 2.9 - - + -
62B LEU* 3.8 20.6 - - + -
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Residues in contact with VAL 471 (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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467A PHE* 2.9 44.6 + - + +
468A GLN* 3.5 7.6 - - - +
470A LEU* 1.3 77.0 - - - +
472A ARG* 1.3 66.8 + - + +
473A GLU 3.1 0.2 + - - -
474A ILE* 3.1 4.7 + - - +
475A ALA* 3.0 22.2 + - - +
484A PHE* 3.8 25.4 - - + -
489A VAL* 4.5 8.3 - - + -
492A LEU* 3.8 27.6 - - + -
62B LEU* 4.8 7.6 - - + -
66B ILE* 3.7 11.1 - - + +
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Residues in contact with ARG 472 (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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468A GLN* 2.9 52.6 + - + +
469A ARG* 3.7 6.5 - - - +
471A VAL* 1.3 84.8 - - + +
473A GLU* 1.3 56.0 + - - +
475A ALA* 3.5 4.9 + - - +
476A GLN* 3.0 27.9 + - - +
482A LEU 4.3 9.3 + - - -
484A PHE* 4.0 35.0 + - + +
489A VAL* 6.2 0.2 - - + -
51I A 2.6 54.4 + - - -
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Residues in contact with GLU 473 (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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469A ARG 2.9 16.6 + - - +
470A LEU* 3.6 12.5 - - - +
472A ARG* 1.3 73.4 - - - +
474A ILE* 1.3 65.7 + - - +
476A GLN* 3.5 12.4 + - - +
477A ASP* 2.8 21.7 - - - +
24B ASP* 4.3 8.0 - - - +
25B ASN* 2.4 47.1 + - - +
26B ILE* 5.4 2.3 + - - +
59B LYS* 6.0 1.4 - - - -
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Residues in contact with ILE 474 (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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470A LEU* 3.0 33.5 + - + +
471A VAL 3.6 3.1 - - - +
473A GLU* 1.3 83.0 - - + +
475A ALA* 1.3 59.3 + - - +
477A ASP* 3.1 26.5 + - - +
478A PHE* 3.7 24.2 - - + -
59B LYS* 4.2 20.9 - - + +
62B LEU* 3.4 39.3 - - + -
63B GLU* 3.9 21.1 - - + +
66B ILE* 3.4 16.8 - - + -
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Residues in contact with ALA 475 (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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471A VAL 3.0 16.4 + - - +
472A ARG 3.7 4.0 - - - +
474A ILE* 1.3 75.5 - - - +
476A GLN* 1.3 53.0 + - - +
477A ASP 2.9 5.6 - - - -
478A PHE* 2.6 27.4 + - - +
479A LYS 3.2 12.7 + - - +
482A LEU* 4.3 5.9 - - + +
484A PHE* 3.7 23.1 - - + -
66B ILE* 3.6 28.0 - - + -
70B VAL* 4.8 4.7 - - + -
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Residues in contact with GLN 476 (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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472A ARG 3.0 17.9 + - - +
473A GLU* 3.6 12.1 - - - +
474A ILE 3.2 0.2 - - - -
475A ALA* 1.3 77.0 - - - +
477A ASP* 1.3 60.4 + - - +
478A PHE 3.2 0.4 - - - -
479A LYS 3.6 9.4 - - - +
480A THR* 3.0 36.1 - - - +
481A ASP* 3.6 18.3 + - - +
482A LEU* 4.6 4.4 + - - +
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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