Contacts of the strand formed by residues 515 - 519 (chain A) in PDB entry 4KSP
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 PHE 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A TRP* 4.1 24.0 - + + -
501A VAL* 4.2 24.2 - - + -
504A LEU* 3.9 42.2 - - + +
505A ARG* 4.1 19.5 - - + -
507A THR* 5.2 1.7 + - - +
513A LEU 3.2 6.7 + - - -
514A LEU* 1.3 74.9 - - - +
516A MET* 1.3 60.3 + - - +
517A GLY* 3.2 43.1 - - - -
518A TYR* 4.1 1.8 - + - -
526A ILE* 4.1 10.3 - - + -
527A VAL 3.9 7.0 - - - -
528A THR* 4.5 5.2 - - - -
508B ARG* 3.1 53.1 + - - +
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Residues in contact with MET 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A TRP* 3.7 22.2 - - - +
451A ILE* 5.3 0.2 - - - +
475A TRP* 3.9 43.0 - - + +
476A HIS 4.9 0.4 - - - +
478A ASP 5.2 0.9 - - - +
479A VAL* 3.8 18.2 - - + -
514A LEU* 3.5 12.8 + - + +
515A PHE* 1.3 80.9 - - - +
517A GLY* 1.3 59.4 + - - +
527A VAL* 3.0 16.2 + - + +
528A THR 3.8 4.3 - - - -
529A GLN* 3.7 26.2 - - - +
508B ARG* 3.5 24.4 - - - +
509B HIS* 3.8 33.0 - - + +
510B VAL* 5.1 6.7 - - + +
565B TYR* 5.1 0.9 + - - -
569B LYS* 5.5 0.2 + - - -
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Residues in contact with GLY 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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449A TRP* 3.5 12.1 - - - -
451A ILE* 3.9 13.7 - - - -
515A PHE* 3.2 25.6 - - - -
516A MET* 1.3 81.9 - - - +
518A TYR* 1.3 60.7 + - - +
526A ILE* 3.7 0.5 - - - -
527A VAL* 2.8 25.9 + - - +
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Residues in contact with TYR 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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448A ASP* 2.9 21.5 + - - -
449A TRP* 3.2 14.3 + - + -
450A GLU* 3.7 38.1 - - + +
451A ILE* 2.9 32.3 + - - +
497A PHE* 3.9 16.8 - + + -
501A VAL* 3.8 34.3 - - + -
505A ARG* 4.8 8.7 + - - -
515A PHE* 4.3 3.6 - + - -
517A GLY* 1.3 75.9 - - - +
519A SER* 1.3 67.3 + - - +
520A THR* 4.2 16.2 - - + -
525A ALA 3.2 13.5 - - - +
526A ILE* 4.4 0.7 - - - +
527A VAL* 4.7 0.9 - - - +
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Residues in contact with SER 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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450A GLU* 5.0 1.5 - - - +
451A ILE 3.7 17.7 + - - -
452A PRO 5.8 0.2 - - - -
453A ASP* 5.0 2.6 - - - -
456A ILE* 4.4 16.8 - - - -
497A PHE* 3.9 1.6 - - - -
518A TYR* 1.3 77.3 - - - +
520A THR* 1.3 69.2 + - - +
521A LYS* 3.4 11.8 + - - +
522A PRO* 3.6 14.7 - - - +
523A GLN 3.2 2.9 - - - +
524A LEU* 3.5 1.2 - - - -
525A ALA* 2.8 44.5 + - - +
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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