Contacts of the helix formed by residues 480 - 497 (chain A) in PDB entry 3APO
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 SER 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A ALA* 3.1 14.6 + - - -
478A PRO 3.1 2.6 - - - -
479A TRP* 1.3 94.0 - - - +
481A PRO* 1.3 68.5 - - - +
482A PRO* 3.4 8.1 - - - +
483A SER* 2.8 39.6 + - - -
484A ARG* 2.9 16.1 + - - +
523A TYR* 3.7 18.5 + - - -
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Residues in contact with PRO 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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44A LYS 3.8 13.7 - - - +
45A THR 3.4 13.5 - - - +
46A ALA 3.2 28.0 - - - +
47A SER* 5.0 4.3 - - - -
48A SER 5.9 0.2 - - - +
93A ARG* 3.7 14.6 - - - +
479A TRP* 3.4 10.0 - - + +
480A SER* 1.3 80.7 - - - +
482A PRO* 1.4 71.8 - - + +
484A ARG* 3.2 22.7 + - - +
485A ALA* 3.1 23.6 + - - +
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Residues in contact with PRO 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 4.1 25.8 - - + +
93A ARG* 4.7 18.6 - - + +
94A LYS* 6.1 5.2 - - + +
97A ASP* 4.6 14.8 - - - +
480A SER* 3.4 9.0 - - - +
481A PRO* 1.4 97.8 - - + +
483A SER* 1.3 63.1 + - - +
485A ALA* 3.6 2.2 + - + +
486A LEU* 3.2 22.5 + - - +
523A TYR 4.4 4.3 - - - +
524A PRO* 4.0 15.7 - - + +
541A HIS* 4.0 10.8 - - + +
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Residues in contact with SER 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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474A ASP* 5.0 1.0 - - - +
476A PHE* 3.5 21.4 - - - +
477A ALA 3.4 15.9 + - - -
480A SER* 2.8 29.0 + - - -
482A PRO* 1.3 77.8 - - - +
484A ARG* 1.3 62.6 + - - +
486A LEU* 3.3 11.3 + - - +
487A LEU* 3.4 19.7 + - - +
523A TYR* 3.4 8.0 - - - +
524A PRO* 3.4 25.5 - - - -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 4.4 7.5 + - - -
47A SER* 5.4 7.9 - - - -
435A HIS* 3.9 13.5 - - + +
436A GLY* 3.7 34.1 - - - +
478A PRO* 3.2 35.1 + - + +
479A TRP* 3.4 22.6 + - - +
480A SER 2.9 9.3 + - - +
481A PRO* 3.2 28.0 + - - +
483A SER* 1.3 76.7 - - - +
485A ALA* 1.3 62.4 + - - +
487A LEU* 3.4 15.0 + - + +
488A PRO* 3.2 19.2 - - - +
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Residues in contact with ALA 485 (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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90A GLU* 3.9 12.8 - - - +
137A ARG* 3.7 32.4 + - - +
481A PRO 3.1 15.1 + - - +
482A PRO* 4.0 1.6 - - + +
484A ARG* 1.3 77.2 - - - +
486A LEU* 1.3 60.7 + - - +
488A PRO* 3.3 14.1 - - - +
489A GLU* 4.1 12.1 - - - +
541A HIS* 5.4 1.1 - - - -
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ASP* 3.6 21.8 - - + +
482A PRO 3.2 14.2 + - - +
483A SER 3.7 8.7 - - - +
484A ARG 3.3 0.2 - - - -
485A ALA* 1.3 76.1 - - - +
487A LEU* 1.3 66.9 + - - +
489A GLU* 2.9 16.2 + - + +
490A LEU* 3.1 18.8 + - + +
524A PRO* 3.7 20.4 - - + -
526A THR* 3.3 25.6 - - - +
537A TYR* 6.0 0.9 - - + -
541A HIS* 3.8 35.5 - - + +
546A ILE* 3.7 29.8 - - + -
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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
----------------------------------------------------------
432A GLU* 5.5 1.3 - - - +
435A HIS* 4.0 31.4 - - + +
455A VAL* 5.4 0.2 - - - +
474A ASP* 3.6 21.8 - - - +
476A PHE* 4.2 18.8 - - + -
483A SER 3.4 14.6 - - - +
484A ARG* 3.7 13.7 - - + +
485A ALA 3.4 0.2 - - - -
486A LEU* 1.3 74.9 - - - +
488A PRO* 1.4 71.4 - - + +
490A LEU* 3.1 9.1 + - - +
491A ARG* 3.0 46.4 + - - +
505A THR* 3.7 22.0 - - + -
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Residues in contact with PRO 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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137A ARG 5.7 1.1 - - - +
138A GLU* 6.3 4.3 - - + -
141A ALA* 6.3 0.4 - - + -
449A GLU* 3.2 34.8 - - - +
484A ARG 3.2 16.2 - - - +
485A ALA* 3.3 12.6 - - - +
487A LEU* 1.4 91.4 - - + +
489A GLU* 1.3 59.4 + - - +
491A ARG* 3.1 11.3 + - + +
492A LYS* 2.9 39.5 + - - +
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Residues in contact with GLU 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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137A ARG* 3.6 30.6 - - - +
485A ALA 4.1 12.6 - - - +
486A LEU* 2.9 10.8 + - + +
488A PRO* 1.3 79.7 - - - +
490A LEU* 1.3 56.8 + - - +
492A LYS* 2.7 32.8 + - - +
493A ALA* 2.9 28.4 + - - +
541A HIS 3.5 22.0 - - - +
542A SER* 3.9 7.1 + - - +
543A ALA* 3.0 39.8 + - - +
546A ILE* 4.4 8.5 - - + -
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A VAL* 4.1 6.1 - - + -
472A LEU* 4.1 22.4 - - + -
474A ASP* 3.9 27.8 - - + +
486A LEU* 3.1 17.2 + - + +
487A LEU* 3.4 11.4 - - - +
489A GLU* 1.3 74.6 - - - +
491A ARG* 1.3 65.2 + - - +
492A LYS 3.2 0.2 - - - -
493A ALA* 3.3 4.4 + - + +
494A SER* 2.9 25.8 + - - -
503A VAL* 3.4 28.2 - - + +
504A GLY 4.4 1.3 - - - +
505A THR* 4.2 16.2 - - + -
526A THR* 4.5 15.0 - - + -
546A ILE* 4.4 17.2 - - + +
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Residues in contact with ARG 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLU* 2.9 36.1 + - - +
433A ILE 5.0 3.0 + - - -
446A PHE* 3.5 33.9 - - - +
449A GLU* 2.9 41.8 + - + -
450A SER* 4.0 7.8 - - - +
453A SER* 3.3 21.0 - - - +
455A VAL* 3.9 10.1 - - + -
487A LEU* 3.0 30.9 + - - +
488A PRO* 3.5 27.1 - - - +
490A LEU* 1.3 75.0 - - - +
492A LYS* 1.3 64.6 + - - +
494A SER* 2.7 23.5 + - - -
495A THR* 3.3 11.7 + - - +
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Residues in contact with LYS 492 (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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137A ARG* 3.3 19.8 + - - +
140A ASP* 6.2 4.7 - - - -
141A ALA* 5.9 5.7 - - - +
449A GLU* 4.4 16.2 + - + +
488A PRO* 2.9 21.7 + - - +
489A GLU* 2.7 43.2 + - - +
490A LEU 3.2 0.4 - - - -
491A ARG* 1.3 75.5 - - - +
493A ALA* 1.3 62.7 + - - +
494A SER 3.2 0.3 + - - -
495A THR* 3.1 24.5 + - - -
496A LEU* 3.8 7.6 + - - +
543A ALA* 3.9 12.3 - - + -
547A LEU* 6.1 0.2 - - - -
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Residues in contact with ALA 493 (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 LEU* 5.5 3.4 - - + -
489A GLU 2.9 16.8 + - - +
490A LEU* 3.8 6.3 - - - +
492A LYS* 1.3 77.0 - - - +
494A SER* 1.3 60.6 + - - +
496A LEU* 3.3 5.6 + - - -
497A LEU* 3.2 31.5 + - + +
543A ALA* 4.2 7.5 - - - +
546A ILE* 4.3 21.1 - - + -
547A LEU* 3.8 28.7 - - + +
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Residues in contact with SER 494 (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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453A SER* 3.5 0.7 - - - -
454A HIS* 3.0 51.6 + - - +
455A VAL* 4.0 2.5 - - - -
490A LEU 2.9 15.0 + - - -
491A ARG* 2.7 19.2 + - - -
492A LYS 3.1 0.2 - - - -
493A ALA* 1.3 75.0 - - - +
495A THR* 1.3 64.2 + - - +
497A LEU* 3.2 11.6 + - - +
498A TYR* 3.4 10.0 + - - -
503A VAL* 3.8 22.2 - - - +
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Residues in contact with THR 495 (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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452A ASN 3.4 25.8 - - - +
453A SER* 3.7 11.4 - - - -
454A HIS* 4.0 9.3 + - + -
491A ARG 3.4 14.6 - - - +
492A LYS* 3.1 14.0 + - - +
494A SER* 1.3 78.8 - - - +
496A LEU* 1.3 68.5 + - - +
497A LEU 3.5 0.5 + - - -
498A TYR* 3.8 12.5 + - - +
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Residues in contact with LEU 496 (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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492A LYS 3.8 5.3 + - - +
493A ALA 3.3 8.6 + - - +
494A SER 3.3 0.4 - - - -
495A THR* 1.3 89.6 + - - +
497A LEU* 1.3 62.6 + - - +
498A TYR 3.4 1.9 + - - +
500A GLN* 4.7 5.7 + - - -
547A LEU* 3.9 32.1 - - + -
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Residues in contact with LEU 497 (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 LEU* 4.6 4.3 - - + -
493A ALA* 3.2 24.2 + - + +
494A SER* 3.2 8.8 + - - +
496A LEU* 1.3 80.3 - - + +
498A TYR* 1.3 66.1 + - - +
499A GLY 3.1 0.7 + - - -
500A GLN* 2.9 46.6 + - + +
501A LEU* 3.1 38.1 + - + +
503A VAL* 4.7 2.9 - - + -
547A LEU* 3.9 19.3 - - + +
550A ILE* 3.5 36.6 - - + -
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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