Contacts of the strand formed by residues 514 - 519 (chain F) in PDB entry 4GDF
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 LEU 514 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286E LEU* 6.3 3.4 - - + -
512E LYS* 2.9 29.9 + - - +
511F LYS* 3.1 39.4 + - + +
512F LYS 2.9 10.1 + - - +
513F HIS* 1.3 86.0 - - + +
515F ASN* 1.3 68.6 + - - +
9G T 5.3 12.3 - - - +
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Residues in contact with ASN 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E PHE* 5.2 1.9 - - - -
511E LYS* 3.5 41.9 - - + +
512E LYS* 2.7 43.9 + - - +
514E LEU* 4.6 6.3 - - - +
509F LEU 4.7 0.9 - - - +
511F LYS* 5.5 3.6 + - - +
513F HIS 5.7 0.2 + - - -
514F LEU* 1.3 83.5 - - - +
516F LYS* 1.3 73.0 + - + +
517F ARG* 3.7 4.7 + - - +
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Residues in contact with LYS 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E LYS* 5.3 5.1 + - - -
452E LEU* 5.5 1.2 - - - +
456E ARG* 4.6 9.9 + - - +
459E PHE* 3.6 30.5 - - + +
460E GLU* 3.3 35.1 + - - +
463E VAL* 3.6 23.3 - - + -
512E LYS* 5.6 3.0 - - - +
508F ASN* 4.1 19.0 + - + +
509F LEU 3.6 8.1 - - - +
510F GLU* 2.9 46.1 + - + +
514F LEU 4.1 0.6 + - - -
515F ASN* 1.3 85.1 - - + +
517F ARG* 1.3 62.4 + - - +
518F THR* 5.2 2.1 + - - +
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Residues in contact with ARG 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E ASP* 4.4 4.2 + - - -
349F ARG* 3.2 52.1 - - - +
352F SER* 5.0 1.8 + - - -
353F LEU* 5.6 5.1 - - - +
465F ILE* 3.9 26.0 - - + +
466F ASP* 2.6 26.4 + - - -
507F VAL 3.4 1.4 - - - +
508F ASN* 3.2 1.6 - - - -
509F LEU* 2.6 43.7 + - - +
515F ASN 4.8 2.7 - - - +
516F LYS* 1.3 77.2 - - - +
518F THR* 1.3 77.1 + - - +
519F GLN* 3.8 20.6 + - + +
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Residues in contact with THR 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E LYS* 3.3 43.6 + - + +
447E ALA 5.8 2.0 - - - +
463E VAL* 5.7 0.5 - - - +
506F LYS* 3.9 29.6 + - + +
507F VAL 3.3 3.6 - - - +
508F ASN* 2.9 24.2 + - - +
516F LYS* 5.2 1.9 - - - +
517F ARG* 1.3 88.5 + - - +
519F GLN* 1.3 66.5 + - - +
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Residues in contact with GLN 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464F ALA 4.5 0.4 + - - -
465F ILE* 3.4 7.8 - - - +
466F ASP* 2.9 31.2 + - - +
467F GLN 5.5 1.6 + - - -
506F LYS* 3.7 13.5 - - - -
507F VAL* 2.7 31.3 + - - +
509F LEU* 3.8 22.9 - - + -
517F ARG* 4.1 23.6 + - + +
518F THR* 1.3 78.6 - - - +
520F ILE* 1.3 90.3 + - + +
521F PHE* 3.9 0.8 - - - +
522F PRO* 3.7 17.4 - - - +
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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