Contacts of the helix formed by residues 478 - 493 (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 SER 478 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B GLU* 5.2 5.8 + - - -
371B SER* 3.5 10.3 + - - -
372B VAL* 3.7 18.0 + - - -
383B TYR* 5.6 0.2 + - - -
477B TYR* 1.3 73.7 - - - +
479B PRO* 1.3 69.1 - - - +
480B GLY* 3.9 2.6 + - - -
481B GLU* 3.2 25.2 + - - +
482B ILE* 2.9 30.0 + - - +
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Residues in contact with PRO 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B TYR 4.1 3.6 - - - +
478B SER* 1.3 86.9 - - - +
480B GLY* 1.3 50.2 + - - +
482B ILE* 3.4 9.7 + - + +
483B ASN* 2.7 53.0 + - - +
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Residues in contact with GLY 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B SER* 3.3 3.5 + - - -
479B PRO* 1.3 77.3 - - - +
481B GLU* 1.3 58.8 + - - +
483B ASN* 3.3 9.3 + - - +
484B ARG* 2.8 29.8 + - - +
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Residues in contact with GLU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASN* 5.0 1.0 + - - -
371B SER* 4.1 7.5 + - - +
383B TYR* 3.5 17.3 + - - +
385B THR* 2.7 34.7 + - - +
386B ARG 4.6 0.3 - - - +
418B THR* 4.9 0.9 - - - -
419B LEU* 4.4 15.8 + - + +
420B TRP* 3.7 17.2 + - - -
477B TYR* 4.9 1.1 - - + -
478B SER* 3.2 25.1 + - - +
480B GLY* 1.3 74.4 - - - +
482B ILE* 1.3 63.3 + - - +
484B ARG* 2.9 32.9 + - - +
485B VAL* 3.1 32.3 + - - +
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 4.0 15.7 - - + -
477B TYR* 3.5 37.7 - - + +
478B SER 2.9 18.9 + - - +
479B PRO* 3.7 8.1 - - + +
481B GLU* 1.3 75.9 - - - +
483B ASN* 1.3 62.9 + - - +
485B VAL* 3.3 2.8 + - - +
486B ALA* 2.9 33.5 + - + +
497B LEU* 5.2 10.6 - - + +
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Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B PRO* 2.7 40.4 + - - +
480B GLY* 3.6 8.0 - - - +
482B ILE* 1.3 80.1 - - - +
484B ARG* 1.3 57.0 + - - +
486B ALA* 3.8 5.0 - - - +
487B SER* 2.9 33.0 + - - -
490B ARG* 4.9 1.0 + - - -
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Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR* 5.6 2.8 + - - -
369B ASN* 2.9 32.2 + - - +
385B THR* 3.4 11.1 - - - +
386B ARG* 3.5 11.1 + - - +
387B ASP* 3.6 48.4 - - - +
388B PRO* 4.6 3.0 - - + +
480B GLY 2.8 19.8 + - - +
481B GLU* 2.9 29.9 + - - +
483B ASN* 1.3 74.7 - - - +
485B VAL* 1.3 62.4 + - - +
487B SER* 3.4 4.9 + - - -
488B CYS* 2.9 22.7 + - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PRO* 4.5 11.2 - - + -
419B LEU* 3.9 29.4 - - + -
420B TRP* 3.9 35.4 - - + -
424B ILE* 4.8 0.2 - - + -
481B GLU* 3.1 23.3 + - - +
482B ILE* 3.7 6.1 - - - +
484B ARG* 1.3 76.8 - - + +
486B ALA* 1.3 64.2 + - - +
488B CYS* 3.0 8.4 + - - +
489B LEU* 2.9 47.6 + - + +
497B LEU* 4.4 7.4 - - + -
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Residues in contact with ALA 486 (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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482B ILE* 2.9 22.2 + - + +
483B ASN* 3.8 6.3 - - - +
485B VAL* 1.3 76.3 - - - +
487B SER* 1.3 62.5 + - - +
489B LEU* 3.3 11.3 + - - +
490B ARG* 3.1 43.1 + - - +
497B LEU* 5.6 5.3 - - + +
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ASN 2.9 18.8 + - - -
484B ARG* 3.7 5.6 - - - -
486B ALA* 1.3 76.8 - - - +
488B CYS* 1.3 62.5 + - - +
490B ARG* 3.3 24.8 + - - +
491B LYS* 3.1 23.9 + - - +
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Residues in contact with CYS 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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387B ASP* 4.8 3.4 - - - +
388B PRO* 3.8 18.4 - - + -
389B THR* 3.4 37.2 - - - +
392B LEU* 3.9 7.9 - - - -
484B ARG 2.9 17.9 + - - +
485B VAL 3.4 4.0 - - - +
487B SER* 1.3 75.6 - - - +
489B LEU* 1.3 57.2 + - - +
491B LYS* 3.2 14.7 + - - +
492B LEU* 2.9 48.2 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.7 21.5 - - + -
424B ILE* 3.6 32.3 - - + -
485B VAL* 2.9 26.9 + - + +
486B ALA* 3.6 9.4 - - - +
487B SER 3.3 0.2 - - - -
488B CYS* 1.3 77.9 - - - +
490B ARG* 1.3 57.5 + - + +
493B GLY* 2.9 10.2 + - - -
494B VAL* 2.8 48.3 + - + +
495B PRO 3.5 20.0 - - - +
496B PRO* 4.3 3.6 - - + -
497B LEU* 3.9 26.0 - - + +
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Residues in contact with ARG 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B HIS* 3.6 11.1 - - - -
483B ASN 4.9 1.4 + - - -
486B ALA* 3.1 32.5 + - - +
487B SER* 3.5 32.2 + - - +
488B CYS 3.3 0.2 - - - -
489B LEU* 1.3 76.3 - - + +
491B LYS* 1.3 62.3 + - - +
493B GLY* 3.4 8.6 + - - -
494B VAL 5.2 0.7 - - - -
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Residues in contact with LYS 491 (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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33B HIS* 2.8 23.8 + - - -
36B MET* 3.1 36.4 - - + +
146B CYS* 4.3 10.2 - - - -
147B VAL 5.6 1.1 - - - +
149B PRO* 6.1 9.1 - - + +
387B ASP* 5.3 2.0 + - - -
389B THR* 2.7 40.2 + - - +
487B SER* 3.1 13.2 + - - +
488B CYS* 3.2 16.4 + - - +
490B ARG* 1.3 78.3 - - - +
492B LEU* 1.3 55.6 + - + +
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Residues in contact with LEU 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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31B LEU* 3.3 26.7 - - + +
33B HIS* 3.2 28.2 + - - +
36B MET* 4.8 7.4 - - + -
37B VAL* 5.2 2.2 - - + -
146B CYS* 3.6 36.3 - - + -
389B THR* 4.0 12.8 - - + +
392B LEU* 3.9 27.4 - - + -
393B ALA* 5.4 0.2 - - + -
488B CYS* 2.9 41.4 + - - +
491B LYS* 1.3 80.5 - - + +
493B GLY* 1.3 62.6 + - - +
494B VAL* 3.7 13.0 - - + -
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Residues in contact with GLY 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.8 0.9 - - - -
32B ARG* 2.9 44.7 + - - +
33B HIS* 3.3 25.0 + - - -
489B LEU 2.9 6.6 + - - -
490B ARG* 3.4 3.3 + - - -
491B LYS 3.3 1.4 - - - -
492B LEU* 1.3 79.2 - - - +
494B VAL* 1.3 61.5 + - - +
495B PRO* 3.9 2.9 - - - +
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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
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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