Contacts of the helix formed by residues 424 - 436 (chain B) in PDB entry 2AX1
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 ILE 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.7 28.3 - - + -
392B LEU* 3.7 19.7 - - + -
420B TRP* 3.0 26.1 + - + +
423B MET* 1.3 80.3 - - - +
425B LEU* 1.3 61.1 + - + +
426B MET 3.4 0.4 - - - -
427B THR* 3.4 1.4 + - - -
428B HIS* 2.8 32.9 + - - +
485B VAL* 4.8 0.2 - - + -
489B LEU* 3.6 42.0 - - + -
494B VAL* 4.3 3.6 - - + -
497B LEU* 4.2 11.4 - - + -
500B TRP* 3.9 26.5 - - + +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 5.7 1.6 - - + -
391B PRO* 4.6 5.4 - - + +
392B LEU* 4.1 17.7 - - + -
395B ALA* 3.9 28.3 - - + -
408B TRP* 4.4 5.2 - - + +
411B ASN* 3.8 22.9 - - + +
412B ILE* 3.8 21.3 - - + +
420B TRP* 3.2 33.3 + - + +
421B ALA* 3.4 16.6 + - + +
424B ILE* 1.3 79.4 - - + +
426B MET* 1.3 58.2 + - - +
428B HIS* 4.7 0.9 - - - -
429B PHE* 2.9 45.7 + - + +
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE* 3.9 30.1 - - + -
416B ALA* 3.9 25.1 - - + +
421B ALA 2.8 16.8 + - - +
422B ARG* 3.3 31.4 - - + +
424B ILE 3.4 0.2 - - - -
425B LEU* 1.3 71.5 - - - +
427B THR* 1.3 63.4 + - - +
430B PHE* 3.0 36.0 + - + +
463B ILE* 3.8 27.8 - - + -
472B PHE* 6.1 0.9 - - + -
525B LEU* 4.1 37.0 - - + +
526B PHE* 3.5 13.1 - - + -
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG 3.9 0.6 + - - -
423B MET 2.8 24.4 + - - -
424B ILE 3.4 1.5 + - - -
425B LEU 3.3 0.4 - - - -
426B MET* 1.3 79.0 - - - +
428B HIS* 1.3 63.7 + - - +
430B PHE* 4.4 0.2 - - - +
431B SER* 3.1 24.9 + - - -
500B TRP* 3.8 18.4 - - + +
503B ARG* 3.9 10.1 - - + -
504B ALA* 3.5 38.2 - - + +
507B VAL* 3.9 7.4 - - + +
526B PHE* 3.4 20.3 - - - -
528B TRP* 3.6 4.7 - - - -
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Residues in contact with HIS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 3.3 26.0 - - - -
29B SER* 4.4 4.9 + - - -
30B LEU* 3.6 35.3 - - + +
399B THR* 2.8 29.2 + - + +
424B ILE 2.8 22.8 + - - +
425B LEU* 3.9 2.2 - - - +
427B THR* 1.3 75.4 - - - +
429B PHE* 1.3 86.2 + + + +
431B SER* 3.3 7.2 + - - -
432B ILE* 3.0 39.7 + - + +
500B TRP* 4.0 17.2 - - + -
503B ARG* 5.6 0.2 + - - -
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Residues in contact with PHE 429 (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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395B ALA* 3.6 28.0 - - + -
398B GLU 5.2 0.9 - - - -
399B THR* 3.5 30.7 - - - -
408B TRP* 3.3 81.2 - + + -
412B ILE* 4.9 1.3 - - + -
425B LEU* 2.9 35.7 + - + +
426B MET* 4.7 0.7 - - - +
428B HIS* 1.3 86.6 - + - +
430B PHE* 1.3 61.9 + - + +
432B ILE* 3.2 14.8 + - + +
433B LEU* 2.8 35.3 + - + +
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Residues in contact with PHE 430 (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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408B TRP* 6.0 1.3 - + - -
412B ILE* 5.4 2.2 - - + -
426B MET* 3.0 36.3 + - + +
429B PHE* 1.3 79.5 - - + +
431B SER* 1.3 63.1 + - - +
433B LEU* 3.8 14.2 - - + +
434B LEU* 2.9 29.6 + - - +
439B LEU* 3.8 27.1 - - + -
456B PRO 3.8 21.8 - - - -
457B LEU* 5.1 0.7 - - + -
459B LEU* 3.7 17.7 - - + -
507B VAL* 3.8 19.3 - - + -
511B LEU* 3.9 17.9 - - + -
521B CYS* 3.9 20.6 - - + -
525B LEU* 3.5 28.5 - - + -
526B PHE* 4.2 8.3 - + + -
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Residues in contact with SER 431 (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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427B THR* 3.1 15.5 + - - -
428B HIS* 3.3 11.4 - - - -
429B PHE 3.1 0.2 - - - -
430B PHE* 1.3 77.6 - - - +
432B ILE* 1.3 64.2 + - - +
434B LEU* 3.3 9.5 + - - +
435B ALA* 3.0 23.0 + - - +
507B VAL* 4.0 19.4 - - - +
510B ARG* 4.5 10.9 + - - +
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Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.0 29.2 - - + +
399B THR* 3.9 26.0 - - + -
428B HIS* 3.0 36.1 + - + +
429B PHE* 3.5 19.1 - - + +
431B SER* 1.3 79.3 - - - +
433B LEU* 1.3 62.3 + - + +
435B ALA* 3.2 5.0 + - + +
436B GLN* 2.9 55.8 + - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 4.2 27.4 - - + -
429B PHE* 2.8 28.5 + - + +
430B PHE* 3.8 18.8 - - + +
432B ILE* 1.3 79.5 - - + +
434B LEU* 1.3 57.9 + - - +
436B GLN* 5.9 0.2 - - - +
437B GLU* 3.0 6.6 + - - -
438B GLN* 2.8 55.1 + - + +
439B LEU* 3.8 27.7 + - + +
443B LEU* 4.7 8.1 - - + -
456B PRO* 4.0 27.6 - - + -
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PHE 2.9 24.2 + - - +
431B SER* 3.5 5.4 - - - +
432B ILE 3.2 0.2 - - - -
433B LEU* 1.3 76.8 - - - +
435B ALA* 1.3 62.5 + - - +
437B GLU* 3.2 14.0 + - - +
439B LEU* 3.8 15.5 - - + -
507B VAL* 4.0 22.0 - - + +
510B ARG* 3.6 50.2 + - + +
511B LEU* 4.0 15.7 - - + +
514B ARG* 3.4 47.8 + - - +
1105B SO4 4.1 4.8 + - - +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 5.5 11.7 - - + -
431B SER 3.0 15.7 + - - +
432B ILE* 3.2 7.8 + - - +
434B LEU* 1.3 77.5 - - - +
436B GLN* 1.3 63.4 + - + +
437B GLU* 3.3 3.7 + - - +
510B ARG* 4.3 7.8 - - - +
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Residues in contact with GLN 436 (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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26B LEU* 4.0 24.1 - - + +
399B THR 5.4 4.4 + - - -
432B ILE* 2.9 32.7 + - + +
433B LEU* 5.9 0.2 - - - +
435B ALA* 1.3 82.0 - - + +
437B GLU* 1.3 71.7 + - - +
438B GLN* 3.3 33.2 + - + +
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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