Contacts of the helix formed by residues 505 - 514 (chain A) in PDB entry 2W3C
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 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A ALA* 4.6 5.6 - - + -
455A LYS* 3.8 31.9 - - + -
456A GLU* 4.3 13.5 - - - -
459A LEU* 5.1 0.2 - - - -
501A TRP 3.7 13.7 - - - +
502A LEU 3.1 17.6 + - - +
504A ASN* 1.3 79.6 - - - +
506A PRO* 1.3 68.7 - - - +
507A ILE* 3.1 18.2 + - - -
508A ALA* 3.2 26.0 + - - +
509A VAL* 3.3 9.2 + - - +
551A PHE* 4.6 1.8 - - - +
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Residues in contact with PRO 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ASN* 3.8 6.3 - - - +
505A CYS* 1.3 87.1 - - - +
507A ILE* 1.3 68.3 + - + +
509A VAL* 3.4 6.3 - - + +
510A THR* 3.2 28.0 + - - -
551A PHE* 3.4 29.3 - - + +
553A ASP* 3.6 32.3 + - + +
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Residues in contact with ILE 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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456A GLU* 4.1 30.3 - - + +
459A LEU* 4.1 9.6 - - + -
505A CYS* 4.1 10.1 - - - -
506A PRO* 1.3 92.4 - - + +
508A ALA* 1.3 58.8 + - - +
509A VAL 3.2 0.2 - - - -
510A THR* 3.2 9.0 + - - -
511A HIS* 2.9 53.6 + - + -
553A ASP* 5.6 2.5 - - - +
1632A PEG 6.4 0.9 - - - -
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Residues in contact with ALA 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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459A LEU* 3.7 34.6 - - + +
475A LEU* 4.3 2.1 - - + +
501A TRP* 4.0 20.0 - - + +
502A LEU* 3.9 13.0 - - + +
505A CYS* 3.2 21.2 + - - +
507A ILE* 1.3 74.9 - - - +
509A VAL* 1.3 59.8 + - - +
511A HIS* 3.5 2.5 + - - +
512A PHE* 3.0 29.5 + - - +
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 3.7 33.2 - - + +
505A CYS 3.5 13.7 - - - +
506A PRO* 3.4 10.3 - - + +
507A ILE 3.2 0.2 - - - -
508A ALA* 1.3 78.8 - - - +
510A THR* 1.3 56.0 + - - +
512A PHE* 3.3 2.4 + - - +
513A LEU* 2.8 52.4 + - + +
547A ILE 4.3 5.2 - - - +
548A SER* 3.4 23.6 - - - +
551A PHE* 4.1 18.4 - - + +
552A ASN* 4.3 11.4 - - - +
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Residues in contact with THR 510 (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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506A PRO 3.2 14.8 + - - -
507A ILE* 3.2 12.7 + - - -
509A VAL* 1.3 77.2 - - - +
511A HIS* 1.3 59.0 + - - +
513A LEU* 3.7 4.7 - - - +
514A HIS* 2.9 32.9 + - - +
553A ASP* 4.3 5.4 + - - -
555A SER* 3.8 18.0 + - - +
556A LEU* 4.0 28.8 + - + +
1632A PEG 4.0 28.5 - - - +
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Residues in contact with HIS 511 (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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459A LEU* 4.2 30.1 - - + +
475A LEU* 3.9 19.2 - - + +
476A GLN* 5.2 1.7 - - - +
507A ILE* 2.9 46.6 + - + +
508A ALA 3.9 4.5 - - - +
509A VAL 3.4 0.2 - - - -
510A THR* 1.3 78.8 - - - +
512A PHE* 1.3 59.3 + - - +
514A HIS* 3.9 13.3 + - - +
515A ASN* 4.1 6.9 + - - +
518A ASN* 5.1 0.2 + - - -
1632A PEG 3.7 43.0 + - - -
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Residues in contact with PHE 512 (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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475A LEU* 4.0 21.3 - - + +
476A GLN* 5.6 0.2 - - - -
479A THR* 3.2 37.0 - - + -
498A LEU* 4.8 2.7 - - + -
502A LEU* 3.8 21.8 - - + -
508A ALA 3.0 18.0 + - - +
509A VAL 3.5 4.0 - - - +
510A THR 3.2 0.2 - - - -
511A HIS* 1.3 77.8 - - - +
513A LEU* 1.3 76.4 + - + +
514A HIS 3.2 1.0 + - - -
515A ASN 3.6 2.6 + - - -
518A ASN* 2.6 54.3 + - + +
519A VAL* 5.5 0.2 - - + -
522A LEU* 3.8 27.1 - - + -
544A LEU* 3.9 27.4 - - + -
548A SER* 4.2 6.1 - - - -
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Residues in contact with LEU 513 (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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509A VAL* 2.8 41.0 + - + +
510A THR* 4.1 1.6 - - - +
512A PHE* 1.3 93.1 - - + +
514A HIS* 1.3 62.3 + - - +
515A ASN 3.4 4.4 + - - +
516A SER* 4.8 0.3 + - - -
519A VAL* 3.5 26.0 - - + -
522A LEU* 6.3 0.2 - - + -
548A SER* 3.8 18.2 - - - +
552A ASN* 3.7 21.1 - - - +
556A LEU* 3.5 21.1 - - + +
558A SER* 4.4 1.6 + - - -
559A TYR* 3.4 40.8 - - + +
564A LEU* 4.2 4.3 - - + -
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Residues in contact with HIS 514 (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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510A THR 2.9 18.6 + - - +
511A HIS* 3.9 9.4 - - - +
512A PHE 3.2 0.4 - - - -
513A LEU* 1.3 76.2 - - - +
515A ASN* 1.3 61.4 + - - +
516A SER* 3.5 4.2 + - - -
556A LEU* 3.7 25.8 - - + +
558A SER* 5.5 0.9 - - - -
1632A PEG 3.7 34.1 + - - +
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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