Contacts of the helix formed by residues 514 - 523 (chain B) 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 SER 514 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A PRO* 4.3 4.9 - - - -
513B PHE* 1.3 76.9 - - - +
515B ARG* 1.3 58.6 + - - +
516B ASN 3.5 3.3 + - - -
517B ASN* 2.8 24.5 + - - +
518B ASN* 2.9 23.6 + - - +
1053D ILE 5.2 0.7 - - - -
1054D TYR* 3.0 34.3 + - - -
1056D PRO* 4.0 18.8 - - - -
1062D ASP* 5.2 0.9 - - - -
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Residues in contact with ARG 515 (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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483A LYS* 3.8 26.6 - - - +
487A LYS* 3.9 12.3 - - - +
502A GLU* 2.8 44.0 + - - +
505A LYS* 3.6 43.8 - - + +
506A ASP* 4.9 3.6 - - + -
507A PRO* 4.1 8.1 - - + +
514B SER* 1.3 69.6 - - - +
516B ASN* 1.3 88.2 + - - +
518B ASN* 3.6 0.7 - - - +
519B ASP* 2.7 50.3 + - - +
1023D CYS* 3.1 19.2 + - - +
1024D ASP* 5.9 0.2 - - - +
1062D ASP* 4.1 16.9 + - - +
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Residues in contact with ASN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B SER* 3.4 2.0 + - - +
515B ARG* 1.3 112.4 - - - +
517B ASN* 1.3 59.0 + - - +
519B ASP* 3.5 5.7 + - - +
520B ARG* 3.3 24.1 + - - +
1023D CYS* 3.7 34.5 + - - +
1053D ILE* 2.9 29.1 - - + +
1054D TYR* 3.8 18.9 - - + -
1062D ASP* 3.7 22.9 + - - +
1067D ILE* 4.6 0.9 - - - +
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Residues in contact with ASN 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B PHE* 4.3 15.7 - - + -
514B SER* 2.8 22.4 + - - +
516B ASN* 1.3 71.6 - - - +
518B ASN* 1.3 62.4 + - - +
520B ARG* 3.3 10.2 + - - +
521B MET* 3.2 28.6 + - - +
527B PRO* 3.2 18.8 - - + +
528B LYS 2.8 45.0 + - - +
1054D TYR* 3.6 27.0 + - - +
1055D TYR* 3.9 8.5 + - - -
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Residues in contact with ASN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER 5.4 0.2 - - - -
505A LYS* 3.1 38.9 - - + +
507A PRO* 4.0 1.0 - - - +
522A LYS* 4.5 3.5 - - - +
504B SER* 4.3 11.9 + - - +
510B SER* 3.3 36.0 + - - +
513B PHE* 3.1 24.0 - - - +
514B SER 2.9 12.6 + - - +
515B ARG 3.9 1.3 - - - +
517B ASN* 1.3 69.2 - - - +
519B ASP* 1.3 65.2 + - - +
521B MET* 3.5 23.4 - - - +
522B LYS* 3.1 24.4 + - - +
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LYS* 2.9 33.8 + - + +
515B ARG* 2.7 43.1 + - - +
516B ASN 3.8 5.5 - - - +
517B ASN 3.2 0.2 - - - -
518B ASN* 1.3 74.6 - - - +
520B ARG* 1.3 60.8 + - - +
522B LYS* 3.8 17.0 + - - +
523B VAL* 4.1 3.3 + - - +
1023D CYS 3.0 19.3 - - - +
1024D ASP* 3.8 3.2 - - - +
1025D ALA* 3.0 31.0 + - - +
1026D ASP 5.6 0.3 + - - -
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Residues in contact with ARG 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ASN 3.3 7.3 + - - +
517B ASN* 3.3 24.0 + - - +
519B ASP* 1.3 75.1 - - - +
521B MET* 1.3 61.0 + - - +
523B VAL* 3.1 14.7 + - - +
525B LYS* 3.0 41.3 + - + +
526B ALA 2.9 32.2 + - - +
528B LYS* 3.7 18.9 - - - +
540B SER* 3.6 13.5 + - - -
1025D ALA* 4.0 15.8 - - + +
1030D GLU* 2.8 39.8 + - - -
1033D LEU* 3.6 17.3 - - + +
1054D TYR* 3.7 22.9 - - + -
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Residues in contact with MET 521 (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 TRP* 3.7 32.5 - - + +
501B GLU* 3.4 16.3 + - - -
503B VAL* 4.0 15.7 - - + -
504B SER* 3.6 15.3 - - - -
513B PHE* 3.7 31.0 - - + -
517B ASN 3.2 18.1 + - - +
518B ASN* 3.5 27.8 - - - +
520B ARG* 1.3 71.8 - - - +
522B LYS* 1.3 66.8 + - - +
523B VAL 3.0 3.1 + - - -
524B GLY 3.0 9.4 + - - -
525B LYS 3.2 17.9 - - - +
527B PRO* 3.8 16.6 - - + -
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Residues in contact with LYS 522 (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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501A GLU* 3.2 32.6 + - - +
504A SER* 6.1 0.2 - - - -
505A LYS* 3.2 27.3 - - + +
522A LYS* 3.4 52.7 - - + +
501B GLU* 3.8 16.4 - - - +
504B SER* 3.8 10.8 + - - -
518B ASN 3.1 16.0 + - - +
519B ASP* 3.8 11.1 + - - +
521B MET* 1.3 75.7 - - - +
523B VAL* 1.4 72.8 + - + +
524B GLY 3.7 0.3 + - - -
1026D ASP* 5.3 7.5 + - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B LYS* 4.4 13.0 + - - +
501B GLU* 4.8 4.3 - - - -
519B ASP 4.6 1.8 - - - +
520B ARG 3.1 14.1 + - - +
521B MET 3.0 0.4 - - - -
522B LYS* 1.4 95.3 - - + +
524B GLY* 1.3 58.7 + - - +
525B LYS* 4.0 27.3 - - + +
1025D ALA* 4.1 15.9 - - + +
1026D ASP* 4.3 23.6 - - - +
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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