Contacts of the helix formed by residues 472 - 490 (chain A) in PDB entry 3PM0
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 GLY 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 4.1 9.6 - - - -
470A CYS* 3.3 10.8 - - - -
471A ILE* 1.3 82.8 - - - +
473A GLU* 1.3 53.0 + - - +
474A GLU 3.6 0.9 - - - -
475A LEU* 3.7 3.5 + - - +
476A SER* 2.7 36.9 + - - -
900A HEM 3.7 25.4 - - - +
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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
----------------------------------------------------------
463A PHE* 3.3 46.8 - - + -
469A ARG* 2.6 31.9 + - - -
470A CYS* 4.0 8.8 - - - +
471A ILE 3.5 3.0 + - - -
472A GLY* 1.3 74.4 - - - +
474A GLU* 1.3 68.7 + - - +
476A SER* 3.1 4.0 + - - -
477A LYS* 3.0 46.0 + - - +
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Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU* 1.3 80.6 - - - +
475A LEU* 1.3 57.7 + - - +
477A LYS* 3.2 12.6 + - + +
478A MET* 2.8 52.1 + - + +
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 4.0 21.3 - - + -
156A PHE* 3.8 29.4 - - + -
166A LEU* 3.9 28.7 - - + -
205A MET* 4.0 24.2 - - + -
208A VAL* 6.2 0.2 - - + -
472A GLY 3.7 7.9 + - - +
473A GLU 3.2 0.6 - - - -
474A GLU* 1.3 77.5 - - - +
476A SER* 1.3 64.1 + - - +
478A MET* 3.6 13.4 + - + +
479A GLN* 3.1 45.5 + - - +
900A HEM 4.4 10.8 - - + -
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.7 20.1 - - - +
463A PHE* 3.7 17.9 - - - -
472A GLY 2.7 17.2 + - - -
473A GLU 3.1 9.4 + - - -
475A LEU* 1.3 80.2 - - - +
477A LYS* 1.3 56.6 - - - +
479A GLN* 3.7 1.4 - - - +
480A LEU* 3.1 35.7 + - - +
900A HEM 3.0 33.1 - - - +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN* 5.5 1.6 - - - -
385A LEU* 5.1 9.5 - - + +
386A TYR* 3.2 38.5 + - + +
389A MET* 4.6 12.8 - - + -
454A LYS* 6.2 0.2 - - - +
463A PHE* 4.4 15.0 - - + -
473A GLU* 3.0 44.4 + - - +
474A GLU* 3.8 11.9 - - + +
476A SER* 1.3 73.0 - - - +
478A MET* 1.3 56.6 + - - +
479A GLN 2.8 10.8 + - - -
480A LEU* 4.0 3.9 - - + +
481A PHE* 3.1 26.7 + - - +
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Residues in contact with MET 478 (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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156A PHE* 4.4 19.3 - - + -
163A ARG* 6.4 2.5 - - - -
166A LEU* 3.6 25.4 - - + +
170A VAL* 5.3 0.3 - - - +
372A MET* 3.5 25.8 - - - +
375A GLN* 4.9 4.0 - - - +
474A GLU* 2.8 50.7 + - + +
475A LEU* 3.7 29.4 - - + +
477A LYS* 1.3 70.7 - - - +
479A GLN* 1.3 56.0 + - - +
481A PHE* 4.5 2.2 - - - -
482A LEU* 3.5 23.7 - - - +
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Residues in contact with GLN 479 (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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166A LEU* 4.6 3.9 - - + +
170A VAL* 3.6 20.0 - - + -
201A VAL* 4.5 4.3 - - - +
204A VAL* 3.5 35.2 - - - +
205A MET* 4.4 3.3 - - - +
335A LEU* 3.3 25.3 - - + +
475A LEU* 3.1 47.2 + - + +
476A SER 3.7 3.8 - - - +
477A LYS 2.8 0.8 - - - -
478A MET* 1.3 79.1 - - - +
480A LEU* 1.3 61.8 + - - +
481A PHE 3.1 1.6 - - - -
482A LEU* 3.4 4.6 + - - +
483A PHE* 2.9 45.3 + - + -
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Residues in contact with LEU 480 (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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201A VAL* 6.2 0.4 - - + -
335A LEU* 4.1 29.2 - - + +
338A ALA* 3.6 26.5 - - + -
339A LEU* 4.1 21.8 - - + +
342A LEU* 4.2 9.9 - - + +
385A LEU* 3.9 25.8 - - + +
389A MET* 5.3 7.2 - - - -
476A SER 3.1 21.1 + - - +
477A LYS* 4.3 3.4 - - + +
479A GLN* 1.3 75.0 - - - +
481A PHE* 1.3 65.2 + - - +
483A PHE* 4.1 5.8 - - + +
484A ILE* 3.3 25.6 + - - +
900A HEM 3.9 17.7 - - + -
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Residues in contact with PHE 481 (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 PRO* 5.7 0.4 - - + -
371A CYS 4.4 9.2 - - - -
372A MET* 2.9 33.7 - - + -
375A GLN* 3.4 33.4 - - + +
378A LEU* 3.4 30.3 - - + -
381A VAL* 3.7 28.7 - - + -
382A LEU* 3.8 23.8 - - + -
385A LEU* 4.5 8.9 - - + +
477A LYS 3.1 17.9 + - - +
478A MET* 4.6 0.9 - - - -
480A LEU* 1.3 79.4 - - - +
482A LEU* 1.3 61.1 + - + +
484A ILE* 3.2 6.0 - - - +
485A SER* 2.8 45.9 + - - -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 6.4 1.1 - - + -
167A GLU* 3.4 49.8 - - + +
170A VAL* 3.6 20.6 - - + -
171A LEU* 6.1 2.5 - - + +
370A PRO 4.2 15.7 - - - +
371A CYS* 4.2 2.2 - - - -
372A MET* 3.5 27.6 - - + +
478A MET 3.5 19.5 - - - +
479A GLN* 3.4 5.8 + - - +
481A PHE* 1.3 81.2 - - + +
483A PHE* 1.3 68.5 + - - +
485A SER* 3.1 4.0 + - - -
486A ILE* 3.0 36.3 + - + +
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Residues in contact with PHE 483 (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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170A VAL* 4.0 17.0 - - + +
173A GLU* 4.0 7.4 - - + -
174A ALA* 3.9 31.2 - - + -
177A LEU* 4.5 13.2 - - + -
200A ALA* 3.9 20.6 - - + -
201A VAL* 4.3 11.9 - - + -
204A VAL* 3.6 32.1 - - + -
335A LEU* 6.3 0.4 - - + -
339A LEU* 3.8 29.4 - - + -
479A GLN* 2.9 43.1 + - + +
480A LEU* 4.6 4.5 - - + +
482A LEU* 1.3 73.9 - - - +
484A ILE* 1.3 62.4 + - - +
486A ILE* 4.0 2.3 - - - +
487A LEU* 2.9 34.6 + - + +
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Residues in contact with ILE 484 (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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339A LEU* 5.6 0.9 - - + -
342A LEU* 3.6 27.4 - - + -
343A LEU* 5.6 2.7 - - + -
346A PHE* 3.7 24.2 - - + -
356A VAL* 5.8 1.8 - - + -
381A VAL* 4.2 18.4 - - + -
384A PHE* 3.0 41.1 - - + -
385A LEU* 4.7 4.9 - - + -
480A LEU 3.3 14.6 + - - +
481A PHE* 3.2 14.4 - - - +
482A LEU 3.1 0.6 - - - -
483A PHE* 1.3 80.4 - - - +
485A SER* 1.3 63.5 + - - +
487A LEU* 4.4 6.5 - - + -
488A ALA* 2.8 36.4 + - + +
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.1 20.7 - - - +
370A PRO* 3.7 23.4 - - - +
381A VAL* 4.1 7.7 - - - +
481A PHE* 2.8 48.8 + - - -
482A LEU* 3.1 7.6 + - - -
484A ILE* 1.3 78.1 - - - +
486A ILE* 1.3 58.9 + - - +
489A HIS* 2.9 27.2 + - - +
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Residues in contact with ILE 486 (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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170A VAL* 5.5 1.1 - - + -
171A LEU* 4.4 16.2 - - + -
174A ALA* 3.9 26.7 - - + -
369A LEU* 4.4 7.9 - - + -
370A PRO* 3.3 38.8 - - + +
482A LEU* 3.0 26.1 + - + +
483A PHE 4.0 2.5 - - - +
485A SER* 1.3 77.3 - - - +
487A LEU* 1.3 56.1 + - + +
489A HIS* 3.2 4.4 + - - +
490A GLN* 2.8 40.6 + - + +
528A LEU* 3.6 33.0 - - + -
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Residues in contact with LEU 487 (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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174A ALA* 4.2 16.6 - - + +
177A LEU* 4.2 24.7 - - + -
178A VAL* 3.4 30.3 - - + -
181A LEU* 5.6 2.7 - - + -
339A LEU* 4.8 7.2 - - + -
343A LEU* 4.5 16.8 - - + -
346A PHE* 5.8 0.2 - - + -
483A PHE* 2.9 33.3 + - + +
484A ILE* 3.9 6.3 - - + +
486A ILE* 1.3 79.3 - - - +
488A ALA* 1.3 54.1 + - - +
490A GLN* 4.5 2.7 - - - +
491A CYS* 2.6 40.2 + - - +
493A PHE* 3.8 23.5 - - + -
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Residues in contact with ALA 488 (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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346A PHE* 3.5 33.4 - - + -
356A VAL* 4.0 10.1 - - + -
357A GLN* 3.0 24.5 + - + +
360A LEU* 3.9 13.5 - - + -
484A ILE 2.8 22.3 + - - +
487A LEU* 1.3 74.4 - - - +
489A HIS* 1.3 59.0 + - - +
491A CYS 3.4 4.6 - - - +
493A PHE* 4.6 1.3 - - - -
523A ARG* 2.8 15.8 + - - -
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Residues in contact with HIS 489 (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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360A LEU* 3.4 15.6 + - + +
361A ASP* 4.6 1.6 + - - -
364A VAL* 3.9 8.4 - - + +
365A GLY 3.5 14.8 - - - -
366A ARG* 2.9 47.1 + - - -
368A ARG 2.9 28.8 + - - -
369A LEU* 3.6 11.7 - - + +
370A PRO* 3.3 20.4 - - + +
485A SER 2.9 23.7 + - - +
486A ILE 3.6 2.0 - - - +
488A ALA* 1.3 74.9 - - - +
490A GLN* 1.3 67.8 + - + +
523A ARG* 2.6 26.6 + - - +
527A GLU* 4.2 8.1 + - - -
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Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 5.2 1.1 - - + -
486A ILE* 2.8 18.6 + - + +
487A LEU* 4.2 1.6 - - - +
489A HIS* 1.3 91.8 - - + +
491A CYS* 1.3 64.2 + - - +
522A LEU* 3.2 31.6 - - + +
523A ARG* 3.2 25.0 + - - +
524A GLU* 3.7 9.3 + - - +
525A SER 4.2 4.6 + - - -
526A MET* 4.3 1.3 - - - +
527A GLU* 3.8 29.5 + - - +
528A LEU* 3.0 51.7 - - + +
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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
------------------------------------------------------------
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