Contacts of the helix formed by residues 498 - 508 (chain B) in PDB entry 5CHG
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 GLU 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468B GLY* 5.7 0.2 - - - -
469B GLN* 3.8 25.4 + - - +
470B GLN* 3.3 15.7 + - - +
494B VAL* 4.9 0.7 - - + -
495B PRO* 3.1 27.5 + - + +
497B SER* 1.3 85.2 - - - +
499B PHE* 1.3 60.6 + - - +
500B ALA 3.4 2.0 - - - -
501B CYS* 3.2 6.9 + - - +
502B ALA* 2.8 28.2 + - - +
529B GLU 3.8 0.2 - - - +
530B HIS* 2.8 59.9 + - - +
531B ALA* 5.9 0.4 - - + -
553B THR* 6.0 0.9 - - - -
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Residues in contact with PHE 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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411B LEU* 4.5 14.1 - - + -
413B VAL* 3.9 26.9 - - + -
431B ALA* 4.7 10.1 - - + -
433B THR* 3.5 30.3 - - + -
494B VAL* 3.8 16.4 - - + -
495B PRO 3.4 4.1 + - - +
496B TYR* 3.2 41.9 + + + +
497B SER 3.5 0.6 - - - -
498B GLU* 1.3 77.1 - - - +
500B ALA* 1.3 54.0 + - - +
502B ALA* 3.1 3.4 + - + +
503B LEU* 2.6 68.5 + - + +
554B PRO 5.8 3.4 - - - +
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Residues in contact with ALA 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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496B TYR 4.8 0.4 + - - -
498B GLU 3.4 0.2 - - - -
499B PHE* 1.3 81.6 - - + +
501B CYS* 1.3 57.9 + - - +
503B LEU* 3.4 7.2 + - - +
504B LEU* 3.0 28.9 + - - +
553B THR* 3.1 31.0 + - - +
554B PRO 4.0 3.7 + - - +
555B THR* 3.4 33.2 - - - +
556B GLU* 3.8 7.2 - - - +
559B VAL* 5.0 2.6 - - + +
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Residues in contact with CYS 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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498B GLU* 3.2 3.1 + - - +
500B ALA* 1.3 76.6 - - - +
502B ALA* 1.3 65.2 + - - +
504B LEU* 3.6 7.2 + - - +
505B TYR* 3.1 23.6 + - - +
527B LEU* 4.1 15.4 - - - +
528B SER 3.8 6.3 - - - +
529B GLU* 3.4 16.0 - - - +
530B HIS 3.6 14.1 - - - +
531B ALA* 3.6 24.5 - - - -
532B LEU* 3.6 11.2 - - - -
553B THR* 3.8 17.6 + - - +
559B VAL* 4.4 11.0 - - - -
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Residues in contact with ALA 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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431B ALA* 5.8 2.7 - - + -
470B GLN* 3.8 3.6 - - - +
494B VAL* 3.8 33.0 - - + -
498B GLU 2.8 17.2 + - - +
499B PHE* 3.4 5.2 - - + +
501B CYS* 1.3 74.8 - - - +
503B LEU* 1.3 65.2 + - - +
505B TYR* 3.3 1.5 + - - +
506B PHE* 2.9 42.3 + - + +
529B GLU 3.2 12.7 + - - +
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Residues in contact with LEU 503 (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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413B VAL* 4.2 17.5 - - + -
415B CYS* 3.7 26.9 - - - -
419B ARG* 3.7 32.1 - - - +
431B ALA* 4.7 3.4 - - + -
499B PHE* 2.6 56.0 + - + +
500B ALA* 3.7 6.7 - - - +
502B ALA* 1.3 71.9 - - - +
504B LEU* 1.3 56.6 + - - +
506B PHE 4.0 0.2 - - - -
507B THR* 2.6 37.7 + - - +
556B GLU* 3.6 10.5 - - + +
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Residues in contact with LEU 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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500B ALA 3.0 17.5 + - - +
501B CYS* 3.8 5.4 - - - +
502B ALA 3.2 0.2 - - - -
503B LEU* 1.3 78.1 - - - +
505B TYR* 1.3 62.4 + - - +
507B THR* 3.5 1.7 + - - -
508B GLY* 3.2 18.9 + - - +
512B PHE* 4.1 17.3 - - + -
513B ASN* 3.6 8.5 - - - +
516B MET* 4.8 8.7 - - + -
527B LEU* 4.3 21.8 - - + -
556B GLU* 3.4 13.4 + - + +
559B VAL* 3.7 35.9 - - + -
560B PHE* 4.1 15.7 - - + -
573B ARG* 3.7 25.6 - - - +
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Residues in contact with TYR 505 (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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501B CYS 3.1 15.1 + - - +
502B ALA 3.3 2.9 + - - +
504B LEU* 1.3 80.7 - - - +
506B PHE* 1.3 89.9 + + - +
508B GLY 3.2 5.4 + - - -
513B ASN* 2.8 36.7 + - + -
517B ARG* 5.7 2.5 - - - -
528B SER* 4.9 4.0 - - - +
529B GLU* 3.9 40.6 - - + -
601B SO4 5.1 1.5 + - - -
603B DGT 3.4 61.2 + + - -
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Residues in contact with PHE 506 (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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415B CYS* 3.5 18.7 - - + +
416B GLY* 3.0 21.0 + - - -
429B ASP* 4.8 5.5 - - + +
431B ALA* 5.2 6.5 - - + -
470B GLN* 4.0 14.8 - - - -
472B LYS* 4.1 21.1 - - + -
492B ILE* 3.7 55.6 - - + -
502B ALA* 2.9 38.1 + - + +
505B TYR* 1.3 100.0 - + - +
507B THR* 1.3 62.5 + - - +
529B GLU* 4.7 5.4 - - + -
603B DGT 3.4 24.0 - + - +
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Residues in contact with THR 507 (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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415B CYS* 4.1 3.8 - - - -
416B GLY* 3.5 9.2 - - - +
419B ARG* 2.8 45.7 + - + +
420B ARG* 2.8 42.8 + - + +
503B LEU 2.6 25.0 + - - -
504B LEU 3.9 4.0 - - - -
506B PHE* 1.3 77.4 - - - +
508B GLY* 1.3 60.9 + - - +
570B PRO* 4.1 10.1 - - + -
573B ARG* 3.8 13.0 - - - +
603B DGT 4.1 0.2 - - - -
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Residues in contact with GLY 508 (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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420B ARG* 4.0 1.6 - - - -
504B LEU 3.2 6.6 + - - +
505B TYR 3.2 15.1 + - - -
507B THR* 1.3 82.2 - - - +
509B SER* 1.3 69.8 + - - -
512B PHE* 3.6 11.4 - - - -
513B ASN* 3.9 3.4 - - - -
573B ARG* 3.6 25.8 - - - +
603B DGT 3.5 8.5 - - - -
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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