Contacts of the helix formed by residues 498 - 508 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A GLN* 4.1 10.9 + - - +
470A GLN* 3.5 12.8 + - - +
494A VAL* 4.2 2.2 - - + -
495A PRO* 2.8 36.9 + - + +
497A SER* 1.3 84.0 - - - +
499A PHE* 1.3 65.1 + - - +
500A ALA 3.2 4.6 + - - -
501A CYS* 3.4 4.7 + - - +
502A ALA* 3.1 21.8 + - - +
529A GLU 3.8 1.9 - - - +
530A HIS* 3.2 53.6 + - - +
531A ALA* 5.5 2.2 - - + +
553A THR* 6.1 0.2 - - - -
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Residues in contact with PHE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LEU* 4.4 15.0 - - + -
413A VAL* 4.3 17.0 - - + -
431A ALA* 4.4 15.5 - - + -
433A THR* 3.5 36.1 - - + -
494A VAL* 3.7 13.5 - - + -
495A PRO 3.2 2.8 + - - +
496A TYR* 3.2 39.5 + + + +
497A SER 3.5 0.2 - - - -
498A GLU* 1.3 78.0 - - - +
500A ALA* 1.3 58.1 + - - +
502A ALA* 3.6 2.2 - - + +
503A LEU* 3.0 66.6 + - + +
554A PRO 5.4 4.9 - - - +
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A TYR 4.7 0.6 + - - -
498A GLU 3.2 1.2 - - - -
499A PHE* 1.3 81.3 - - - +
501A CYS* 1.3 62.5 + - - +
503A LEU* 3.8 7.4 - - - +
504A LEU* 3.1 23.6 + - - +
553A THR* 3.1 30.6 + - - +
554A PRO 3.8 7.4 + - - +
555A THR* 3.6 28.0 - - - +
556A GLU* 3.8 9.9 - - - +
559A VAL* 4.5 4.7 - - + -
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Residues in contact with CYS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A GLU* 3.4 3.4 + - - +
500A ALA* 1.3 80.3 - - - +
502A ALA* 1.3 59.7 + - - +
504A LEU* 3.7 8.3 - - - +
505A TYR* 3.2 23.7 + - - +
527A LEU* 4.1 10.1 - - - -
528A SER 3.4 17.7 - - - +
529A GLU* 3.5 16.2 - - - +
530A HIS 3.8 8.5 - - - +
531A ALA* 3.6 7.6 - - - -
532A LEU* 3.6 27.6 - - - -
553A THR* 3.9 17.2 + - - -
559A VAL* 4.4 10.5 - - - -
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ALA* 5.6 4.9 - - + -
470A GLN* 4.4 0.9 - - - +
492A ILE* 4.8 6.3 - - + -
494A VAL* 3.7 31.9 - - + -
498A GLU 3.1 16.7 + - - +
499A PHE* 3.6 7.0 - - + +
500A ALA 3.1 0.2 - - - -
501A CYS* 1.3 75.6 - - - +
503A LEU* 1.3 65.5 + - - +
505A TYR* 3.2 4.1 + - - +
506A PHE* 3.0 27.6 + - - +
529A GLU* 3.4 14.8 + - - +
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A VAL* 4.2 12.8 - - + -
415A CYS* 3.6 29.4 - - - -
419A ARG* 4.3 17.9 - - - +
431A ALA* 4.2 4.0 - - + -
499A PHE* 3.0 63.4 + - + +
500A ALA* 3.8 5.6 - - - +
502A ALA* 1.3 76.4 - - - +
504A LEU* 1.3 56.8 + - - +
507A THR* 2.5 38.1 + - - -
556A GLU* 4.0 18.2 - - + +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ALA 3.1 15.0 + - - +
501A CYS* 3.7 7.2 - - - +
503A LEU* 1.3 79.1 - - - +
505A TYR* 1.3 62.6 + - - +
507A THR* 4.1 1.2 - - - -
508A GLY 3.3 16.8 + - - +
512A PHE* 4.9 4.1 - - + -
513A ASN* 3.5 10.5 - - - +
516A MET* 3.7 33.2 - - + -
527A LEU* 4.1 14.6 - - + -
556A GLU* 3.5 22.1 + - + +
559A VAL* 3.8 23.3 - - + -
560A PHE* 4.1 15.9 - - + -
573A ARG* 3.4 27.7 + - - +
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Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A LYS* 3.2 18.2 + - + -
492A ILE* 5.2 3.6 - - + -
501A CYS 3.2 16.0 + - - +
502A ALA 3.2 3.3 + - - +
504A LEU* 1.3 80.9 - - - +
506A PHE* 1.3 99.0 + + - +
508A GLY 3.6 0.2 + - - -
513A ASN* 2.7 30.3 + - - +
517A ARG* 3.2 30.1 - - - +
529A GLU* 3.4 30.1 - - + -
5P A 2.7 35.9 + + - -
6P C 3.2 35.2 - - - +
6T G 4.0 2.5 - - - -
7T T 4.8 1.3 - - - -
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A CYS* 2.6 31.6 - - + +
429A ASP* 3.6 37.2 - - + -
430A VAL 4.7 2.9 - - - -
431A ALA* 5.1 1.8 - - + -
472A LYS* 3.5 31.4 - - + -
490A ASP* 4.3 14.6 - - + -
492A ILE* 3.7 43.7 - - + -
502A ALA 3.0 14.3 + - - +
503A LEU 4.3 0.4 - - - +
505A TYR* 1.3 113.0 - + - +
507A THR* 1.3 58.4 + - - +
5P A 5.3 3.4 - - + -
6P C 3.0 31.0 - - - +
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Residues in contact with THR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A CYS* 3.4 13.6 + - - +
416A GLY 3.3 5.0 - - - +
419A ARG* 2.7 58.2 + - + +
420A ARG* 2.8 35.1 + - + +
503A LEU* 2.5 29.8 + - - -
504A LEU 4.1 2.0 - - - -
506A PHE* 1.3 72.3 - - - +
508A GLY* 1.3 61.6 + - - +
570A PRO* 4.1 7.0 - - + -
573A ARG* 4.1 11.2 - - - +
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Residues in contact with GLY 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ARG* 4.1 2.0 - - - -
504A LEU 3.3 7.3 + - - +
506A PHE 3.2 2.4 - - - -
507A THR* 1.3 82.7 - - - +
509A SER* 1.3 68.1 + - - -
512A PHE* 3.2 19.0 - - - -
513A ASN* 3.5 10.9 - - - +
573A ARG* 3.4 17.5 - - - +
6P C 3.2 13.5 - - - -
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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