Contacts of the helix formed by residues 515 - 525 (chain A) in PDB entry 5K7W
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 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A ARG* 3.9 19.1 + - - +
512A HIS* 5.4 7.7 - - - +
513A LYS 4.6 6.1 - - - +
514A PRO* 1.3 68.1 - - - +
516A GLU* 1.3 70.6 + - - +
517A ILE 3.0 3.3 + - - -
518A TYR* 3.1 41.0 + - + +
519A GLY 4.1 1.7 + - - -
538A HIS* 4.6 16.6 - - - +
539A ASN* 5.3 0.5 + - - -
541A GLN* 4.6 7.9 + - - +
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Residues in contact with GLU 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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503A ILE* 4.1 12.6 - - + -
504A VAL 4.5 4.5 - - - +
505A ALA* 3.8 12.7 - - - +
508A ARG* 3.1 39.7 + - - -
514A PRO* 3.1 7.5 - - + +
515A ASP* 1.3 75.3 + - - +
517A ILE* 1.3 62.0 + - - +
519A GLY* 3.1 12.4 + - - +
520A MET* 3.2 15.9 + - - +
523A ARG* 4.8 1.4 + - - -
117B ASN 4.0 14.2 - - - +
118B ASP* 3.4 36.3 - - - +
119B TYR 4.8 1.5 + - - +
120B CYS* 3.8 21.6 - - - -
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Residues in contact with ILE 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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393A MET* 4.1 26.2 - - + -
429A PHE* 4.5 11.2 - - + -
431A TRP* 4.7 19.3 - - + +
455A ILE* 3.9 24.9 - - + -
483A CYS* 5.3 1.1 - - - -
503A ILE* 3.9 23.6 - - + +
513A LYS* 5.7 2.9 - - + -
514A PRO 3.3 17.5 + - - +
515A ASP 3.0 1.4 - - - -
516A GLU* 1.3 79.7 - - - +
518A TYR* 1.3 77.9 + - + +
520A MET* 3.4 11.1 + - + +
521A ILE* 3.0 37.3 + - + +
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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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393A MET* 3.6 18.9 - - + +
513A LYS 6.1 0.2 - - - -
514A PRO 5.0 0.9 - - - -
515A ASP* 3.1 40.2 + - + +
517A ILE* 1.3 83.5 - - + +
519A GLY* 1.3 58.4 + - - +
521A ILE* 3.4 4.8 + - - +
522A GLU* 2.9 30.5 + - - +
532A GLU* 2.5 32.4 + - - -
539A ASN* 2.9 32.9 + - - +
541A GLN* 3.7 42.4 - - + +
544A TRP* 3.8 29.4 + + - +
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Residues in contact with GLY 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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515A ASP 4.1 1.6 + - - -
516A GLU* 3.1 7.6 + - - +
518A TYR* 1.3 77.4 - - - +
520A MET* 1.3 65.2 + - - +
522A GLU* 3.8 5.4 - - - +
523A ARG* 2.9 47.7 + - - +
118B ASP* 5.5 3.8 - - - -
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Residues in contact with MET 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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455A ILE* 3.9 21.1 - - + -
499A ASP* 3.7 31.7 - - + +
500A CYS 3.5 24.7 - - - +
503A ILE* 3.6 36.1 - - + -
516A GLU 3.2 11.4 + - - +
517A ILE* 3.4 12.8 + - + +
519A GLY* 1.3 75.9 - - - +
521A ILE* 1.3 57.4 + - + +
523A ARG* 3.4 6.7 + - - +
524A LEU* 3.0 27.1 + - - +
120B CYS* 3.8 11.7 - - - -
281B PHE* 3.8 27.4 - - + -
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Residues in contact with ILE 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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391A VAL* 3.8 17.5 - - + -
393A MET* 4.0 16.2 - - + -
429A PHE* 3.7 39.5 - - + -
517A ILE* 3.0 38.3 + - + +
518A TYR 3.9 3.6 - - - +
520A MET* 1.3 74.1 - - + +
522A GLU* 1.3 61.3 + - - +
524A LEU* 3.2 8.8 + - + +
525A SER* 2.9 27.5 + - - +
530A LYS* 3.7 29.2 - - + -
544A TRP* 3.9 17.7 - - + -
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Residues in contact with GLU 522 (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 TYR 2.9 18.5 + - - +
519A GLY* 3.3 7.2 + - - +
521A ILE* 1.3 77.4 - - - +
523A ARG* 1.3 58.4 + - + +
525A SER 4.3 0.9 - - - -
526A PRO* 3.0 36.9 - - + +
527A GLY 2.9 29.5 + - - -
530A LYS* 3.1 26.2 + - - +
542A PRO 5.1 0.9 - - - +
543A ASN* 3.3 21.0 + - - +
544A TRP* 4.6 7.4 + - - -
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Residues in contact with ARG 523 (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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495A ASN* 3.1 25.3 + - - +
498A LEU* 3.6 21.2 - - + +
499A ASP* 2.8 43.8 + - - +
516A GLU 4.8 0.6 + - - -
519A GLY* 2.9 31.9 + - - +
520A MET 3.5 16.2 - - - +
522A GLU* 1.3 75.7 - - + +
524A LEU* 1.3 65.4 + - - +
525A SER 3.6 0.2 + - - -
526A PRO* 3.8 4.1 - - - +
118B ASP* 5.0 4.0 + - - -
120B CYS* 3.6 20.8 - - - +
121B GLN* 3.3 28.6 - - - +
124B VAL* 3.6 27.6 - - - +
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Residues in contact with LEU 524 (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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391A VAL* 5.3 2.2 - - + -
427A PHE* 4.1 21.8 - - + -
429A PHE* 3.9 27.8 - - + -
494A PHE* 3.2 23.2 - - + -
495A ASN 2.9 51.1 + - - +
498A LEU* 5.8 0.6 - - - +
520A MET 3.0 14.3 + - - +
521A ILE* 3.2 9.8 + - - +
523A ARG* 1.3 78.4 - - - +
525A SER* 1.3 60.6 + - - +
526A PRO* 3.6 2.2 - - - +
280B VAL* 3.5 37.0 - - + +
281B PHE* 4.3 8.1 - - + -
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Residues in contact with SER 525 (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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390A ALA* 3.7 8.5 - - - +
391A VAL* 4.1 12.8 - - - -
427A PHE* 5.6 2.9 - - - -
493A GLY 4.6 5.0 + - - -
494A PHE* 5.2 5.0 - - - +
521A ILE 2.9 10.6 + - - -
522A GLU 3.3 3.7 - - - +
524A LEU* 1.3 82.9 - - - +
526A PRO* 1.3 63.9 - - - +
528A THR* 2.7 32.9 + - - +
530A LYS* 2.8 31.5 + - - -
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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