Contacts of the helix formed by residues 450 - 464 (chain B) in PDB entry 2JA7
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 ALA 450 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B PHE* 3.3 42.8 - - + +
167B ILE* 3.9 2.7 - - - +
168B GLY* 3.1 29.1 - - - +
424B LEU* 5.3 4.3 - - - -
448B ILE* 2.6 15.2 + - - +
449B ASN* 1.3 66.8 - - - +
451B LYS* 1.3 57.6 + - - +
452B THR 3.4 1.3 - - - -
453B ILE* 4.6 2.5 - - - +
454B THR* 2.9 22.0 + - - -
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Residues in contact with LYS 451 (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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449B ASN* 2.5 30.6 + - - +
450B ALA* 1.3 74.9 - - - +
452B THR* 1.3 55.2 + - - +
453B ILE 3.4 0.2 - - - -
454B THR* 4.0 6.3 - - - -
455B SER* 2.7 48.4 + - - +
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Residues in contact with THR 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 4.8 22.1 - - + +
423B LYS* 4.6 22.9 - - + -
424B LEU* 4.2 19.1 - - + +
427B ASP* 5.3 5.1 + - - +
449B ASN* 3.0 24.7 + - - +
451B LYS* 1.3 79.3 - - - +
453B ILE* 1.3 64.4 + - + +
455B SER* 3.2 11.6 + - - -
456B GLY* 3.2 11.1 + - - -
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Residues in contact with ILE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.8 6.5 - - + -
167B ILE* 3.3 42.6 - - + +
168B GLY* 4.2 7.2 - - - -
169B ARG 5.0 0.7 - - - +
417B PHE* 3.7 38.1 - - + -
420B LEU* 4.5 18.3 - - + +
421B PHE* 4.9 5.4 - - + -
424B LEU* 3.6 19.7 - - + -
450B ALA* 4.3 2.6 + - - +
452B THR* 1.3 76.5 - - + +
454B THR* 1.3 68.3 + - - +
455B SER 3.2 0.3 + - - -
457B LEU* 3.1 40.3 + - + +
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 4.6 2.1 - - - -
168B GLY* 3.0 1.6 - - - -
169B ARG* 2.7 63.1 + - + +
171B PRO* 5.3 0.7 - - - +
450B ALA 2.9 19.0 + - - -
451B LYS* 3.6 8.2 + - - -
453B ILE* 1.3 79.3 - - - +
455B SER* 1.3 62.9 + - - +
457B LEU* 4.0 3.3 + - - +
458B LYS* 3.5 31.7 + - - +
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LYS* 2.7 37.8 + - - +
452B THR* 3.2 5.9 + - - -
454B THR* 1.3 74.0 - - - +
456B GLY* 1.3 62.6 + - - +
457B LEU 3.2 1.8 - - - -
458B LYS* 2.6 34.1 + - - +
459B TYR* 2.9 13.4 + - - +
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Residues in contact with GLY 456 (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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416B LEU* 5.3 1.9 - - - +
420B LEU* 4.4 17.7 - - - -
452B THR 3.2 12.2 + - - -
453B ILE 4.0 0.2 - - - -
455B SER* 1.3 81.3 + - - +
457B LEU* 1.3 63.3 + - - +
459B TYR* 3.2 9.5 + - - +
460B ALA* 3.0 23.1 + - - +
468B GLU* 6.0 5.0 - - - -
469B GLN* 6.1 4.0 - - - -
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 5.6 0.7 - - + -
169B ARG 3.5 11.4 - - - +
170B LEU* 3.8 17.0 - - + -
171B PRO* 3.4 34.2 - - + +
413B LEU* 4.2 26.0 - - + +
416B LEU* 4.3 22.7 - - + -
417B PHE* 4.8 11.2 - - + +
420B LEU* 4.1 8.7 - - + +
453B ILE* 3.1 31.8 + - + +
454B THR 4.0 2.2 - - - +
456B GLY* 1.3 74.4 - - - +
458B LYS* 1.3 63.7 - - - +
460B ALA* 3.5 5.5 - - - +
461B LEU* 3.2 23.9 + - - +
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Residues in contact with LYS 458 (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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123B THR* 3.5 35.5 + - + +
125B SER* 6.1 0.9 - - - -
169B ARG* 6.4 0.4 - - - +
171B PRO* 5.2 4.2 - - + +
205B ILE* 4.5 18.8 - - + +
206B ASN* 3.7 28.3 + - - +
454B THR* 3.5 26.2 - - - +
455B SER* 2.6 19.4 + - - +
457B LEU* 1.3 70.4 - - + +
459B TYR* 1.3 70.1 + - - +
460B ALA 2.8 0.9 + - - -
461B LEU 2.9 3.6 + - - -
462B ALA* 2.7 26.8 + - + +
958B GLN* 5.1 9.9 + - - +
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Residues in contact with TYR 459 (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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272 A 4.9 19.9 - - - -
455B SER 2.9 9.7 + - - +
456B GLY* 3.5 12.6 - - - +
458B LYS* 1.3 74.4 - - - +
460B ALA* 1.3 64.3 + - - +
462B ALA* 3.2 5.7 + - - +
463B THR* 2.7 46.8 + - + +
465B ASN* 3.8 30.7 + - + +
468B GLU* 3.5 25.0 + - - -
469B GLN* 3.2 47.3 - - + +
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Residues in contact with ALA 460 (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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416B LEU* 3.5 32.3 - - + -
456B GLY 3.0 11.1 + - - +
457B LEU 3.5 9.0 - - - +
458B LYS 2.8 3.8 + - - -
459B TYR* 1.3 73.1 - - - +
461B LEU* 1.3 55.5 + - + +
462B ALA 2.7 15.1 + - - -
464B GLY* 3.0 24.3 + - - -
465B ASN 4.0 13.0 - - - -
466B TRP* 3.6 22.7 - - + +
468B GLU* 6.3 0.2 - - - -
480B SER* 4.1 0.2 + - - -
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Residues in contact with LEU 461 (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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171B PRO* 4.5 7.4 - - + -
203B PHE* 3.5 52.0 - - + -
205B ILE* 4.0 18.4 - - + +
210B LYS* 2.9 21.2 - - + +
212B LEU* 3.9 13.5 - - + -
413B LEU* 3.8 18.8 - - + -
416B LEU* 4.4 1.1 - - + -
457B LEU* 3.2 17.9 + - + +
458B LYS 2.9 5.5 + - - -
460B ALA* 1.3 76.9 - - + +
462B ALA* 1.3 54.9 + - - +
466B TRP* 3.2 25.1 - - + -
480B SER* 2.7 25.8 + - - +
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Residues in contact with ALA 462 (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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262 C 3.1 32.6 - - - +
272 A 5.7 0.7 - - - +
205B ILE* 4.0 15.9 - - + -
206B ASN* 5.7 3.6 - - + +
210B LYS* 3.0 23.2 - - - +
458B LYS* 2.7 24.6 + - + +
459B TYR* 3.4 8.7 - - - +
460B ALA 2.7 2.8 + - - -
461B LEU* 1.3 76.3 - - - +
463B THR* 1.3 58.9 + - - +
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Residues in contact with THR 463 (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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252 T 6.1 0.7 - - - +
262 C 4.7 19.7 + - - +
272 A 5.0 6.8 + - - -
53 C 5.4 4.0 + - - -
210B LYS* 5.4 0.3 - - - -
459B TYR* 2.7 31.1 + - + +
462B ALA* 1.3 82.0 - - - +
464B GLY* 1.3 60.3 + - - +
465B ASN* 3.7 30.7 + - - +
477B ALA* 5.7 0.2 - - - +
478B GLY 5.3 0.3 + - - -
480B SER 3.7 11.4 - - - +
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Residues in contact with GLY 464 (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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460B ALA 3.0 10.7 + - - -
463B THR* 1.3 78.7 - - - +
465B ASN* 1.3 64.5 + - - +
466B TRP* 2.9 11.1 + - - -
476B ARG 3.3 6.4 - - - +
477B ALA* 3.3 16.2 - - - -
478B GLY 3.4 7.6 + - - -
479B VAL* 2.9 31.4 + - - +
480B SER* 3.9 0.9 - - - -
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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
------------------------------------------------------------
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