Contacts of the helix formed by residues 492 - 504 (chain B) in PDB entry 5EMQ
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 CYS 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A ASN* 4.5 6.3 - - + +
476B CYS* 3.9 18.6 - - - -
477B ALA 4.8 0.2 - - - -
482B CYS* 3.8 14.6 - - + -
484B ILE* 3.7 6.5 - - + +
488B ARG 4.1 1.6 + - - -
489B ARG 3.9 5.3 + - - -
490B LYS 3.5 0.4 - - - -
491B ASN* 1.3 83.8 - - + +
493B PRO* 1.3 60.3 - - - +
494B ALA* 3.2 4.3 - - - -
495B CYS* 3.2 17.9 + - + -
496B ARG* 2.9 27.9 + - - +
602B ZN 2.3 38.4 - - - -
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Residues in contact with PRO 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ASN* 4.9 9.2 - - - +
463B PHE* 3.6 15.2 - - + -
474B TYR* 3.5 40.8 - - + -
489B ARG 4.6 1.5 - - - +
490B LYS 3.9 7.0 - - - +
491B ASN 3.5 9.0 - - - +
492B CYS* 1.3 86.5 - - - +
494B ALA* 1.3 53.9 + - - +
496B ARG* 3.1 3.6 + - + +
497B TYR* 2.7 37.1 + - - +
11C A 5.0 1.6 - - - +
12C T 3.5 20.6 - - - +
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TYR* 3.6 31.8 - - + +
475B LEU 4.0 2.6 + - - -
476B CYS* 3.9 28.7 - - + +
480B ASN* 5.9 1.1 - - - +
492B CYS* 3.2 5.5 - - - -
493B PRO* 1.3 79.3 - - - +
495B CYS* 1.3 57.8 + - - +
497B TYR* 3.4 4.0 + - - +
498B ARG* 3.0 27.6 + - - +
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Residues in contact with CYS 495 (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 CYS* 3.9 1.6 - - - -
480B ASN* 3.5 15.0 - - - -
482B CYS* 3.4 17.0 - - + +
484B ILE* 4.0 16.4 - - + -
492B CYS* 3.2 9.5 + - + +
494B ALA* 1.3 76.3 - - - +
496B ARG* 1.3 65.7 + - - +
498B ARG* 3.2 32.6 + - - +
499B LYS* 2.9 27.4 + - - +
602B ZN 2.5 33.7 - - - -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B VAL* 4.0 5.5 - - + +
459B SER* 3.9 1.0 + - - -
460B CYS* 3.1 44.8 - - - +
463B PHE* 3.3 48.8 - - + +
484B ILE* 3.8 23.0 - - + +
489B ARG* 3.5 44.0 + - - +
490B LYS 5.0 0.4 - - - +
492B CYS 2.9 17.8 + - - +
493B PRO* 3.6 4.3 - - + +
495B CYS* 1.3 77.6 - - - +
497B TYR* 1.3 56.0 + - - +
499B LYS* 3.2 4.9 + - - +
500B CYS* 3.0 27.8 + - - -
12C T 4.1 10.7 + - - -
13C G 2.5 31.7 + - - -
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Residues in contact with TYR 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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463B PHE* 3.7 10.3 - + + -
464B PHE* 4.1 14.8 - + - -
467B ALA* 3.5 22.9 - - + -
468B VAL* 3.7 35.3 - - + +
472B HIS* 4.2 22.5 - + - -
474B TYR* 4.4 8.7 - + + -
493B PRO 2.7 21.8 + - - +
494B ALA* 3.7 5.4 - - - +
496B ARG* 1.3 71.8 - - - +
498B ARG* 1.3 64.6 + - - +
500B CYS* 3.2 6.9 + - - +
501B LEU* 3.0 52.0 + - + +
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Residues in contact with ARG 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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480B ASN* 2.9 32.6 + - - -
481B ASP* 3.7 8.8 - - - +
482B CYS 4.9 3.2 + - - -
494B ALA 3.0 14.6 + - - +
495B CYS* 3.2 37.9 - - - +
496B ARG 3.3 0.2 - - - -
497B TYR* 1.3 77.8 - - - +
499B LYS* 1.3 79.8 + - - +
501B LEU* 3.3 12.2 + - - +
502B GLN* 2.9 59.0 + - + +
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Residues in contact with LYS 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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441B LEU 3.9 10.7 + - - +
442B VAL* 2.6 43.5 + - + +
443B CYS* 4.8 0.6 - - - +
444B SER* 5.6 2.6 + - - -
482B CYS 5.3 1.8 - - - +
484B ILE* 3.5 37.9 + - + +
495B CYS 2.9 9.3 + - - +
496B ARG 3.2 7.8 + - - +
498B ARG* 1.3 98.8 - - - +
500B CYS* 1.3 63.9 + - - +
502B GLN* 3.8 11.1 - - - +
503B ALA* 2.9 26.2 + - - +
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Residues in contact with CYS 500 (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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442B VAL* 4.0 13.2 - - - +
460B CYS* 4.6 4.7 - - - -
463B PHE* 4.2 17.0 - - - -
464B PHE* 3.6 30.5 - - + -
496B ARG 3.0 22.7 + - - -
497B TYR* 3.2 10.5 - - - +
499B LYS* 1.3 78.2 - - - +
501B LEU* 1.3 59.7 + - - +
503B ALA* 3.4 3.3 + - - +
504B GLY 3.3 3.3 + - - -
505B MET* 3.1 55.1 + - + +
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Residues in contact with LEU 501 (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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464B PHE* 4.1 16.2 - - + -
497B TYR* 3.0 56.4 + - + +
498B ARG* 3.7 9.6 - - - +
500B CYS* 1.3 73.4 - - - +
502B GLN* 1.3 67.1 + - - +
504B GLY* 2.9 16.0 + - - +
505B MET 4.3 10.0 - - - +
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Residues in contact with GLN 502 (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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498B ARG* 2.9 60.4 + - + +
499B LYS* 3.3 10.4 + - - +
501B LEU* 1.3 76.3 - - + +
503B ALA* 1.3 61.0 + - - +
504B GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 4.2 23.8 - - + +
442B VAL* 4.6 7.2 - - + -
454B VAL* 3.3 33.1 - - + +
499B LYS 2.9 18.3 + - - +
500B CYS 3.7 5.8 - - - +
501B LEU 3.1 0.2 - - - -
502B GLN* 1.3 76.0 - - - +
504B GLY* 1.3 58.7 + - - +
505B MET* 3.6 0.7 - - + -
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Residues in contact with GLY 504 (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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453B GLY* 5.4 0.3 - - - -
454B VAL* 3.7 7.0 - - - +
501B LEU 2.9 13.0 + - - -
502B GLN 3.1 1.9 - - - -
503B ALA* 1.3 80.2 - - - +
505B MET* 1.3 62.7 + - - +
506B ASN* 2.8 23.2 + - - +
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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