Contacts of the helix formed by residues 494 - 507 (chain A) in PDB entry 4X8G
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 PRO 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ALA 4.2 3.8 - - - +
493A SER* 1.3 84.6 - - - +
495A ARG* 1.3 59.5 + - - +
497A CYS* 3.2 2.3 + - + +
498A TYR* 2.9 38.5 + - + -
539A ASN* 3.3 46.0 - - + +
542A VAL* 4.2 12.1 - - + -
543A GLU* 3.9 27.6 - - + +
546A ILE* 4.6 5.6 - - + -
569A GLN 3.1 17.7 - - - +
570A LEU* 4.9 0.7 - - - -
571A PHE* 5.0 2.2 - - + -
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 3.2 8.2 + - - +
494A PRO* 1.3 79.8 - - - +
496A SER* 1.3 61.6 + - - +
498A TYR* 3.5 5.2 + - - +
499A LYS* 3.2 25.8 + - + +
540A SER* 5.9 1.2 + - - -
543A GLU* 3.2 38.9 + - - +
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 3.2 28.5 + - - -
494A PRO 3.2 0.2 - - - -
495A ARG* 1.3 78.7 - - - +
497A CYS* 1.3 60.6 + - - +
499A LYS* 3.6 2.8 + - - +
500A LEU* 3.6 8.7 + - - +
566A ASP* 3.8 15.1 + - - -
568A PRO* 3.6 19.3 - - - +
615A LYS* 2.6 46.6 + - - +
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Residues in contact with CYS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER 3.2 3.7 + - - +
494A PRO 3.2 7.2 + - - +
496A SER* 1.3 78.0 - - - +
498A TYR* 1.3 63.9 + - - +
500A LEU* 3.5 4.2 + - - +
501A PHE* 3.3 47.9 + - - -
568A PRO* 3.7 8.3 - - + +
569A GLN 3.4 24.9 - - - +
570A LEU* 3.6 32.8 - - + -
583A PHE* 4.2 13.9 - - - -
612A LEU* 4.4 6.5 - - - -
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Residues in contact with TYR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A PRO* 2.9 28.7 + - + +
495A ARG* 4.0 6.5 - - - +
497A CYS* 1.3 73.8 - - - +
499A LYS* 1.3 61.0 + - - +
501A PHE* 3.3 5.4 + - - +
502A GLN* 2.9 31.8 + - - +
529A ILE 4.5 3.7 + - - -
530A LEU* 3.7 26.8 - - + +
535A LEU* 3.4 17.3 + - + +
536A ARG* 3.2 68.2 + - + +
539A ASN* 3.4 30.4 + - + -
570A LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ARG* 3.2 20.0 + - + +
496A SER* 3.9 6.7 - - - +
497A CYS 3.3 0.4 - - - -
498A TYR* 1.3 76.7 - - - +
500A LEU* 1.3 56.6 - - - +
502A GLN* 3.5 4.9 + - - +
503A GLU* 2.9 33.8 + - + +
615A LYS* 4.6 8.3 - - - +
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A SER 3.6 9.1 + - - +
497A CYS* 3.5 8.8 + - - +
498A TYR 3.3 0.4 - - - -
499A LYS* 1.3 79.3 - - - +
501A PHE* 1.3 59.5 + - + +
503A GLU* 3.2 7.0 + - + +
504A GLN* 2.9 58.5 + - + +
568A PRO* 5.6 0.4 - - + -
611A CYS* 3.6 40.4 - - + +
612A LEU* 3.7 27.1 - - + -
615A LYS* 4.3 27.3 - - + +
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Residues in contact with PHE 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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497A CYS* 3.3 26.9 + - - +
498A TYR* 3.3 8.4 + - - +
500A LEU* 1.3 86.4 - - + +
502A GLN* 1.3 57.3 + - - +
504A GLN* 3.5 4.1 + - - -
505A GLN 3.0 20.8 + - - -
526A ILE* 3.2 51.9 - - + +
529A ILE* 4.9 13.5 - - + -
530A LEU* 3.5 18.9 - - + +
570A LEU* 5.7 7.0 - - + -
583A PHE* 5.9 2.2 - + - -
604A PRO* 3.9 26.9 - - + -
611A CYS* 4.8 4.0 - - - -
612A LEU* 3.9 30.1 - - + -
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Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A TYR 2.9 17.0 + - - +
499A LYS* 4.0 5.4 - - - +
501A PHE* 1.3 76.5 - - - +
503A GLU* 1.3 62.4 + - - +
505A GLN* 2.9 25.7 + - - +
506A ASN* 2.9 50.5 + - - +
530A LEU* 3.7 21.3 - - + +
536A ARG* 3.9 25.7 - - - +
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Residues in contact with GLU 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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499A LYS* 2.9 22.7 + - + +
500A LEU* 3.2 8.5 + - + +
502A GLN* 1.3 77.5 - - - +
504A GLN* 1.3 62.9 + - + +
506A ASN* 3.6 9.4 + - - +
507A GLU* 3.1 24.0 + - - +
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Residues in contact with GLN 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 LEU* 2.9 42.6 + - + +
501A PHE* 3.9 4.3 - - - +
502A GLN 3.3 0.2 - - - -
503A GLU* 1.3 78.9 + - - +
505A GLN* 1.3 62.0 + - - +
506A ASN 3.3 0.7 - - - -
507A GLU* 3.2 18.7 + - - +
509A HIS* 3.1 30.0 + - - +
510A GLY* 4.8 0.2 - - - -
526A ILE* 4.3 9.0 - - + -
606A ILE* 3.3 46.6 - - + +
611A CYS* 4.7 6.6 - - + +
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Residues in contact with GLN 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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501A PHE 3.0 17.9 + - - +
502A GLN* 2.9 35.4 + - - +
503A GLU 3.3 0.2 - - - -
504A GLN* 1.3 76.4 - - - +
506A ASN* 1.3 63.9 + - - +
508A GLY* 3.3 12.6 + - - -
510A GLY* 3.9 19.6 + - - -
526A ILE* 4.4 2.7 - - + -
527A LYS* 3.3 32.3 - - + +
530A LEU* 3.5 15.5 - - + +
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Residues in contact with ASN 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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502A GLN* 2.9 37.9 + - - +
503A GLU* 3.8 9.3 - - - +
504A GLN 3.3 0.2 - - - -
505A GLN* 1.3 78.5 + - - +
507A GLU* 1.3 58.8 + - - +
508A GLY* 3.1 3.7 + - - -
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Residues in contact with GLU 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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503A GLU 3.1 16.8 + - - +
504A GLN* 3.5 24.2 - - - +
505A GLN 3.2 1.0 - - - -
506A ASN* 1.3 76.2 - - - +
508A GLY* 1.3 55.1 + - - +
509A HIS* 3.3 7.4 + - + +
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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