Contacts of the helix formed by residues 506 - 511 (chain A) in PDB entry 3GKL
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 ASP 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A ARG* 3.1 37.2 + - - +
480A ILE* 4.1 5.6 - - + +
502A GLU 3.3 12.5 + - - +
503A VAL 3.4 2.5 + - - +
505A LYS* 1.3 76.1 - - - +
507A PRO* 1.3 69.8 - - - +
508A GLU* 2.5 38.1 + - - +
509A LEU* 2.9 30.6 + - + +
510A SER* 2.9 22.2 + - - -
515B ARG* 4.9 5.4 - - + -
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Residues in contact with PRO 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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505A LYS 3.2 10.7 - - - +
506A ASP* 1.3 84.7 - - - +
508A GLU* 1.3 70.5 + - + +
510A SER* 3.5 9.5 + - - +
511A LYS* 3.6 5.5 - - - +
510B SER 3.9 2.7 - - - +
511B LYS* 3.2 46.7 - - - +
513B PHE 3.2 27.8 - - - +
514B SER* 4.5 3.6 - - - -
515B ARG* 4.1 10.8 - - + +
518B ASN* 4.0 0.2 - - - +
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Residues in contact with GLU 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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461A ASN 5.0 0.3 - - - +
462A ASN* 5.0 0.3 - - - -
479A ARG* 4.0 23.6 - - - +
506A ASP* 2.5 16.4 + - - +
507A PRO* 1.3 94.5 - - + +
509A LEU* 1.3 58.8 + - - +
511A LYS* 3.3 38.8 + - - +
512A GLN* 3.1 19.6 + - - -
511B LYS* 4.1 14.4 - - - +
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Residues in contact with LEU 509 (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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460A VAL* 3.9 28.0 - - + -
461A ASN 4.8 0.4 - - - +
464A TRP* 4.3 17.5 - - + -
477A PRO* 4.0 10.3 - - + -
479A ARG* 4.0 5.6 - - - +
480A ILE* 3.5 38.1 - - + -
503A VAL* 4.1 21.5 - - + +
506A ASP* 2.9 19.6 + - + +
508A GLU* 1.3 79.7 - - - +
510A SER* 1.3 60.4 + - - +
511A LYS 3.1 1.6 - - - -
512A GLN* 2.8 42.0 + - - +
513A PHE* 3.4 10.8 - - + -
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Residues in contact with SER 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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503A VAL 3.7 5.2 + - - -
504A SER 3.3 25.1 - - - -
505A LYS 5.0 0.2 - - - -
506A ASP 2.9 21.9 + - - -
507A PRO* 3.5 6.6 + - - +
509A LEU* 1.3 74.4 - - - +
511A LYS* 1.3 62.0 + - - +
512A GLN 3.1 1.3 + - - -
513A PHE* 3.2 19.8 + - - +
518A ASN* 3.3 23.7 + - - +
507B PRO* 3.6 2.4 - - - +
510B SER* 2.7 31.3 + - - -
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Residues in contact with LYS 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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462A ASN* 4.0 25.1 - - - +
507A PRO 3.6 12.5 + - - +
508A GLU* 3.3 52.2 + - - +
509A LEU 3.0 1.0 + - - -
510A SER* 1.3 80.9 + - - +
512A GLN* 1.3 61.2 + - + +
513A PHE 3.4 0.2 - - - -
507B PRO* 3.6 32.4 - - - +
508B GLU* 4.4 10.0 - - - +
511B LYS* 3.9 16.8 - - + +
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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