Contacts of the helix formed by residues 487 - 500 (chain B) in PDB entry 2A1A
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 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 4.3 13.0 - - + +
75A VAL 5.1 0.2 - - - -
76A ASP* 3.8 26.4 + - + +
81A TYR* 3.4 23.7 - - + +
83A ASP* 3.2 21.5 - - - +
382B ARG* 3.3 6.8 + - - +
485B CYS* 3.2 0.9 - - - +
486B ASP* 1.3 85.0 - - + +
488B ALA* 1.3 60.1 + - - +
489B PHE 3.9 0.4 - - - -
490B GLU* 3.1 28.9 + - - +
491B THR* 2.9 28.1 + - - -
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 3.6 20.6 - - + +
46A LEU* 3.9 21.8 - - + -
74A ARG* 5.1 1.6 - - - +
83A ASP* 2.7 18.3 + - - +
379B GLU* 5.7 1.1 - - - +
382B ARG* 3.6 16.9 - - - +
487B THR* 1.3 68.5 - - - +
489B PHE* 1.3 65.8 + - - +
491B THR* 2.9 11.9 + - - -
492B SER* 2.8 20.8 + - - -
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Residues in contact with PHE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.5 29.4 - + - -
42A GLU* 3.6 30.3 - - + -
43A GLY* 3.8 24.0 - - - -
44A MET* 3.6 22.3 - - + +
80A GLY 5.2 0.9 - - - -
81A TYR* 3.5 41.1 - + + -
82A ILE 3.5 25.4 - - - +
83A ASP* 2.7 21.3 + - - +
487B THR* 4.3 0.4 - - - -
488B ALA* 1.3 73.9 - - - +
490B GLU* 1.3 60.9 + - - +
492B SER* 3.1 13.3 + - - -
493B LYS* 3.3 20.7 + - - +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP* 4.2 4.2 - - - +
79A LYS* 2.9 44.6 + - - +
81A TYR* 3.7 24.8 - - + +
483B HIS* 3.3 18.9 + - - -
485B CYS* 3.9 14.8 - - - -
486B ASP 3.5 16.5 + - - -
487B THR* 3.1 24.0 + - - +
489B PHE* 1.3 73.2 - - - +
491B THR* 1.3 60.5 + - - +
493B LYS* 3.5 3.8 + - + +
494B PHE* 2.9 28.1 + - + +
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Residues in contact with THR 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 6.4 0.9 - - + -
382B ARG* 3.0 23.1 + - - +
453B ARG* 3.6 27.8 - - - +
480B GLU* 4.3 9.4 - - + +
485B CYS* 3.3 20.0 - - + +
487B THR 2.9 16.1 + - - -
488B ALA* 2.9 10.8 + - - -
490B GLU* 1.3 75.8 - - - +
492B SER* 1.3 64.8 + - - +
494B PHE* 3.3 1.1 + - + +
495B PHE* 3.1 34.1 + - + -
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 6.0 0.9 - - - +
29A MET* 3.2 30.7 - - - +
32A TYR* 3.1 24.6 + - - -
44A MET* 3.5 11.3 - - - +
453B ARG* 5.7 2.9 - - - +
488B ALA 2.8 9.0 + - - -
489B PHE 3.3 9.4 - - - -
491B THR* 1.3 78.1 - - - +
493B LYS* 1.3 64.9 + - - +
495B PHE* 3.1 11.9 + - - +
496B THR* 3.2 16.6 + - - -
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Residues in contact with LYS 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 4.0 22.1 - - - -
42A GLU* 4.6 7.3 + - - -
81A TYR* 3.8 30.5 - - + +
489B PHE* 3.3 37.0 + - + +
490B GLU* 3.9 5.2 - - + +
492B SER* 1.3 74.0 - - - +
494B PHE* 1.3 64.3 + - - +
496B THR* 3.2 12.8 + - - -
497B ASP* 3.0 27.9 + - - +
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Residues in contact with PHE 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ALA* 3.7 21.8 - - + -
480B GLU* 3.9 23.3 - - + -
483B HIS* 4.0 24.5 - + + -
485B CYS* 3.9 22.7 - - - -
490B GLU* 2.9 20.8 + - + +
491B THR* 3.3 5.4 - - + +
492B SER 3.1 0.2 + - - -
493B LYS* 1.3 74.6 - - - +
495B PHE* 1.3 80.8 + + - +
497B ASP* 3.2 16.0 - - + +
498B LEU* 3.2 49.1 + - + +
504B SER* 5.6 4.9 - - - -
506B ILE* 5.2 1.1 - - + -
507B PHE* 3.8 21.1 - + - -
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Residues in contact with PHE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ARG* 3.4 46.0 - - + +
454B TYR* 3.3 44.0 - + - -
476B LEU* 3.7 30.5 - - + +
480B GLU* 3.4 23.8 - - + -
491B THR* 3.1 28.4 + - + +
492B SER* 3.1 8.7 + - - +
494B PHE* 1.3 88.7 - + - +
496B THR* 1.3 56.5 + - - +
498B LEU* 2.9 8.7 + - + +
499B ARG* 2.8 43.1 + - + +
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Residues in contact with THR 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.5 1.6 + - - -
492B SER 3.2 14.7 + - - -
493B LYS* 3.2 14.1 + - - -
495B PHE* 1.3 76.2 - - - +
497B ASP* 1.3 66.2 + - - +
499B ARG* 3.4 22.9 + - + +
500B ASP* 3.5 16.3 - - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B LYS* 3.0 16.4 + - - +
494B PHE* 3.2 16.7 - - + +
496B THR* 1.3 79.7 - - - +
498B LEU* 1.3 62.6 + - + +
500B ASP* 3.5 2.6 - - - +
501B GLY 3.3 3.1 + - - -
502B ILE* 2.8 66.9 + - + +
504B SER* 5.8 3.3 - - - -
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B LEU* 3.8 21.1 - - + -
479B ALA* 3.7 29.8 - - + -
494B PHE* 3.3 43.7 - - + +
495B PHE* 2.9 15.3 + - + +
497B ASP* 1.3 69.6 - - + +
499B ARG* 1.3 66.7 + - - +
501B GLY* 2.7 14.9 + - - +
502B ILE 3.6 15.7 - - - +
503B ILE* 4.2 17.5 - - + -
504B SER 5.4 0.4 - - - +
507B PHE* 4.7 5.4 - - + -
515B LEU* 6.0 0.4 - - + -
519B LEU* 3.1 30.7 - - + +
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Residues in contact with ARG 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LEU* 3.1 29.7 + - - +
453B ARG* 4.4 6.7 - - - +
454B TYR 3.7 7.1 - - - +
455B MET 2.3 33.9 + - - +
456B SER 5.8 0.2 - - - -
457B PRO* 5.6 4.4 - - - +
460B ILE* 3.4 17.2 - - - +
472B TYR* 3.8 31.0 + - - -
476B LEU* 4.2 7.4 - - + +
495B PHE* 2.8 32.4 + - + +
496B THR* 3.4 12.5 + - - +
498B LEU* 1.3 72.8 - - - +
500B ASP* 1.3 62.8 + - + +
501B GLY 3.5 1.6 + - - -
519B LEU* 4.8 2.6 - - - +
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Residues in contact with ASP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B THR* 3.5 19.3 - - - +
497B ASP 3.6 2.2 + - - +
498B LEU 3.2 0.6 - - - -
499B ARG* 1.3 77.7 - - + +
501B GLY* 1.3 55.8 + - - +
502B ILE* 3.1 33.6 + - - +
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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
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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