Contacts of the helix formed by residues 488 - 502 (chain B) in PDB entry 5CTR
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 ASN 488 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B ARG* 4.5 9.3 - - - +
482B GLU* 3.0 45.3 + - - +
483B ALA* 4.5 0.6 - - - +
486B CYS* 3.8 8.3 - - + +
487B ASN* 1.3 74.9 - - - +
489B MET* 1.3 63.8 + - - +
490B GLN* 3.3 4.8 - - - +
491B LYS* 2.9 34.5 + - - +
492B ALA 3.9 1.9 + - - -
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Residues in contact with MET 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ALA* 3.7 23.7 + - + +
487B ASN* 3.6 5.6 + - - +
488B ASN* 1.3 76.7 - - - +
490B GLN* 1.3 62.1 + - - +
492B ALA* 3.2 10.8 + - + +
493B ARG* 3.0 57.6 + - + +
514B TYR* 4.2 8.7 - - + -
517B LEU* 4.2 12.6 - - + +
518B GLU* 3.2 41.5 - - - +
521B HIS* 4.0 28.7 - - + +
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Residues in contact with GLN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASN* 3.3 5.7 - - - +
489B MET* 1.3 78.4 - - + +
491B LYS* 1.3 62.6 + - - +
493B ARG* 3.0 33.0 + - - +
494B GLU* 3.0 24.0 + - - +
526B HIS* 5.2 1.6 + - - -
27D THR* 5.8 4.5 - - - -
28D LEU* 4.5 20.2 + - + +
130D HIS* 3.7 10.4 - - - +
131D CYS* 3.0 53.3 + - + +
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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
----------------------------------------------------------
478B TRP* 3.9 33.4 - - + -
482B GLU* 3.6 16.2 - - + +
488B ASN* 2.9 23.3 + - - +
490B GLN* 1.3 79.1 - - - +
492B ALA* 1.3 52.1 + - - +
494B GLU* 2.8 41.9 + - - +
495B LEU* 2.7 62.1 + - + +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ALA* 3.6 40.6 - - + +
482B GLU* 4.7 1.4 - - + +
483B ALA* 3.9 15.9 - - + +
488B ASN 3.9 3.2 + - - +
489B MET* 3.2 15.8 + - + +
491B LYS* 1.3 80.0 - - - +
493B ARG* 1.3 57.1 + - - +
495B LEU* 3.5 1.8 - - - +
496B TRP* 2.8 35.8 + - - +
517B LEU* 4.3 7.2 - - + -
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Residues in contact with ARG 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET* 3.0 37.0 + - + +
490B GLN* 3.0 39.5 + - - +
492B ALA* 1.3 74.6 - - - +
494B GLU* 1.3 53.5 + - - +
496B TRP* 3.2 2.3 + - - -
497B ASP* 2.8 35.5 + - - +
514B TYR* 3.6 18.2 - - - +
518B GLU* 2.6 32.7 + - - +
522B GLY* 3.8 10.7 - - - -
523B ASP* 4.3 2.4 + - - +
526B HIS* 3.5 39.5 + - - -
128D VAL* 3.5 15.9 - - + +
129D LYS 4.3 5.2 - - - +
130D HIS* 3.7 15.0 - - + +
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Residues in contact with GLU 494 (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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490B GLN 3.0 12.4 + - - +
491B LYS* 2.8 42.1 + - - +
493B ARG* 1.3 77.1 - - - +
495B LEU* 1.3 62.2 + - + +
497B ASP* 3.5 2.9 + - - +
498B SER* 3.2 21.1 + - - -
130D HIS* 3.5 31.0 - - + +
131D CYS 5.6 0.9 - - - +
132D LYS* 3.0 31.5 + - - +
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Residues in contact with LEU 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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453B LEU* 4.8 0.4 - - + -
475B MET* 3.6 35.9 - - + +
478B TRP* 3.7 38.6 - - + +
479B ALA* 3.5 38.8 - - + +
482B GLU* 5.0 0.7 - - + -
491B LYS* 2.7 48.6 + - + +
492B ALA 3.2 4.9 + - - +
494B GLU* 1.3 74.7 - - + +
496B TRP* 1.3 58.7 + - - +
498B SER* 3.1 5.7 + - - -
499B ILE* 2.9 31.6 + - - +
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Residues in contact with TRP 496 (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 GLN* 3.5 40.9 + - + +
479B ALA* 3.8 19.0 - - + +
480B ARG* 6.0 0.2 - - - -
492B ALA 2.8 25.3 + - - +
493B ARG 3.8 3.4 - - - +
495B LEU* 1.3 71.8 - - - +
497B ASP* 1.3 59.4 + - - +
499B ILE* 3.5 25.2 - - + +
500B MET* 2.8 56.6 + - + +
510B MET* 3.5 39.9 - - + -
513B GLU* 3.9 17.9 - - + -
514B TYR* 3.8 35.9 - + + +
517B LEU* 3.7 19.4 - - + +
128D VAL* 3.9 8.3 - - + -
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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 ARG 2.8 16.3 + - - +
494B GLU 3.7 1.3 - - - +
496B TRP* 1.3 71.9 - - - +
498B SER* 1.3 54.1 + - - +
500B MET* 3.4 2.6 + - - +
501B THR* 2.6 46.1 + - - -
125D GLY* 3.3 0.9 - - - -
126D LEU* 3.2 28.2 + - - +
127D PHE 3.3 15.9 + - - -
128D VAL* 3.2 33.3 - - - +
130D HIS* 2.9 27.9 - - + -
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B MET* 3.5 21.3 - - - +
494B GLU 3.2 10.7 + - - -
495B LEU 3.1 8.4 + - - -
496B TRP 3.1 0.4 - - - -
497B ASP* 1.3 80.9 - - - +
499B ILE* 1.3 61.7 + - - +
501B THR* 3.3 10.9 - - - +
502B ARG* 3.1 38.6 + - - +
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Residues in contact with ILE 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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471B SER 4.1 0.7 - - - +
472B CYS* 3.7 17.3 - - + +
475B MET* 3.6 34.8 - - + +
476B GLN* 3.5 28.9 - - + +
495B LEU 2.9 27.3 + - - +
496B TRP* 3.1 41.7 + - + +
498B SER* 1.3 76.2 - - - +
500B MET* 1.3 59.8 + - - +
502B ARG* 3.5 7.8 + - - +
504B ASN* 2.9 41.9 + - + +
510B MET* 3.8 7.9 - - + -
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Residues in contact with MET 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B TRP* 2.8 33.5 + - + +
497B ASP 3.8 0.2 - - - +
499B ILE* 1.3 74.1 - - - +
501B THR* 1.3 63.5 + - - +
503B GLY* 3.3 2.3 + - - -
504B ASN* 3.2 38.4 + - - +
505B ALA* 3.3 17.5 + - + +
510B MET* 3.4 42.0 - - + +
511B TRP* 3.5 29.2 - - + +
514B TYR* 4.5 4.0 - - + -
127D PHE* 3.8 31.5 - - + -
128D VAL* 4.2 13.0 - - + -
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Residues in contact with THR 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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497B ASP* 2.6 35.2 + - - -
498B SER* 3.3 13.8 - - - +
500B MET* 1.3 74.2 - - - +
502B ARG* 1.3 61.2 + - - +
503B GLY* 2.8 12.8 + - - -
126D LEU* 3.6 23.5 - - + +
127D PHE* 3.7 15.9 - - + -
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Residues in contact with ARG 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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457B LYS* 4.3 29.6 - - - +
467B SER* 5.6 11.6 - - - +
469B ASP 6.0 0.2 - - - +
470B PRO 5.0 5.5 - - - +
472B CYS* 4.1 24.7 - - - -
475B MET* 5.2 6.8 - - - -
498B SER* 3.1 30.2 + - - +
499B ILE 3.9 7.0 - - - +
500B MET 3.3 1.2 - - - -
501B THR* 1.3 76.8 - - - +
503B GLY* 1.3 59.6 + - - +
504B ASN* 3.5 5.1 + - - +
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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