Contacts of the strand formed by residues 514 - 521 (chain A) in PDB entry 5FM8
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ALA* 4.1 10.3 - - + +
513A PRO* 1.3 80.2 - - - +
515A ASP* 1.3 75.9 + - - +
516A VAL* 3.4 4.3 + - - -
530A TRP* 3.6 2.8 - - - +
531A LYS* 2.8 45.9 + - + +
532A GLN 4.6 11.0 - - - +
533A PRO* 5.1 1.1 - - + -
534A ALA* 5.2 11.7 - - + +
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Residues in contact with ASP 515 (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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514A LEU* 1.3 83.1 - - - +
516A VAL* 1.3 67.0 + - - +
517A LYS* 3.2 24.7 + - + +
529A SER 3.7 4.9 - - - +
530A TRP* 3.7 4.2 - - - -
531A LYS* 2.9 39.5 + - + +
596A SER* 5.6 0.8 - - - -
597A ARG* 6.2 1.6 - - - +
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Residues in contact with VAL 516 (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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514A LEU 4.6 1.1 - - - +
515A ASP* 1.3 72.4 - - - +
517A LYS* 1.3 65.8 + - - +
528A ILE* 4.0 24.2 - - + -
529A SER 3.3 10.1 - - - +
530A TRP* 4.0 8.3 - - + -
582A PHE* 4.2 9.4 - - + +
583A ARG* 4.7 0.4 - - - -
584A VAL* 3.7 19.5 - - + +
596A SER* 3.2 34.5 - - - +
597A ARG 4.0 8.6 + - - +
598A VAL 5.2 0.2 - - - -
599A SER* 3.9 33.9 - - - +
600A GLU 5.0 0.9 + - - -
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Residues in contact with LYS 517 (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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515A ASP* 3.2 29.4 - - + +
516A VAL* 1.3 77.2 - - - +
518A CYS* 1.3 63.1 + - - +
519A LEU* 4.5 9.7 - - + +
528A ILE* 3.1 10.8 - - - +
529A SER* 2.8 44.6 + - - +
531A LYS* 5.8 4.3 - - - +
599A SER* 5.2 4.3 - - - -
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Residues in contact with CYS 518 (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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517A LYS* 1.3 75.6 - - - +
519A LEU* 1.3 66.8 + - - +
520A GLU* 3.5 29.2 - - - -
521A ALA* 4.1 2.0 - - - -
526A ILE* 3.8 16.8 - - - -
527A ILE 3.4 4.7 - - - +
528A ILE* 4.3 4.3 - - + -
599A SER* 5.9 0.6 - - - -
602A VAL* 3.8 32.3 - - + -
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Residues in contact with LEU 519 (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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517A LYS* 4.5 12.8 - - - +
518A CYS* 1.3 78.4 - - - +
520A GLU* 1.3 64.0 + - + +
527A ILE* 2.8 33.5 + - + +
529A SER* 3.4 35.7 - - - +
568A ARG* 4.5 12.8 - - + -
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Residues in contact with GLU 520 (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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518A CYS* 3.5 7.6 - - - -
519A LEU* 1.3 83.4 - - + +
521A ALA* 1.3 68.9 + - - +
522A ASN* 4.7 3.0 + - - +
525A TYR* 3.6 21.0 + - + +
526A ILE* 3.5 1.6 - - - -
527A ILE* 2.9 53.6 + - + +
520C GLU* 3.9 18.9 - - - +
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Residues in contact with ALA 521 (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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518A CYS* 4.1 3.3 - - - -
520A GLU* 1.3 80.5 - - - +
522A ASN* 1.3 64.3 + - - +
525A TYR 3.8 4.5 - - - -
526A ILE* 3.9 7.4 - - + -
602A VAL* 3.5 32.3 - - + -
603A ALA 4.0 9.2 - - - +
605A LEU 3.8 6.4 - - - +
607A PRO* 3.8 15.9 - - - +
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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