Contacts of the helix formed by residues 560 - 568 (chain A) in PDB entry 5C16
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLY* 3.4 35.2 - - - -
227A TRP* 3.7 28.7 - - - +
471A GLU* 4.7 0.2 + - - -
538A PHE* 3.1 14.1 - - - -
540A THR* 3.6 9.1 + - - -
559A ILE* 1.3 73.9 - - - +
561A LEU* 1.3 66.1 + - - +
562A TRP* 3.2 20.8 + - - -
563A SER* 3.2 18.3 + - - -
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Residues in contact with LEU 561 (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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528A THR* 4.8 1.1 - - + -
529A ILE* 4.1 18.8 - - + -
532A HIS* 3.8 23.1 - - + -
538A PHE* 3.4 37.7 - - + -
540A THR* 2.9 22.1 + - - +
541A PHE* 3.7 26.9 - - + -
560A SER* 1.3 71.4 - - - +
562A TRP* 1.3 88.5 + - + +
564A TYR* 3.2 13.8 + - + +
565A ILE* 3.1 25.6 + - + +
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Residues in contact with TRP 562 (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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226A GLY* 3.9 20.6 - - - -
229A VAL* 4.1 5.2 - - + -
467A GLU* 3.3 62.0 - - + +
470A VAL* 4.4 18.4 - - + -
471A GLU* 2.7 37.5 + - + +
525A PHE* 4.3 1.3 - + - -
529A ILE* 3.7 30.1 - - + -
540A THR* 4.2 16.3 - - + +
541A PHE* 4.6 5.4 - + - -
560A SER* 3.1 15.8 - - - +
561A LEU* 1.3 98.7 - - + +
563A SER* 1.3 61.1 + - - +
565A ILE* 3.8 14.8 - - + +
566A ASN* 2.8 38.4 + - - +
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Residues in contact with SER 563 (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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222A PHE* 3.8 19.5 - - - -
224A ILE* 3.2 21.0 + - - +
225A ASN* 3.6 4.7 + - - -
226A GLY* 2.6 28.4 + - - +
559A ILE* 4.1 5.0 - - - +
560A SER* 3.4 18.4 + - - -
561A LEU 3.2 0.6 - - - -
562A TRP* 1.3 78.5 - - - +
564A TYR* 1.3 60.1 + - - +
566A ASN* 4.6 0.3 - - - +
567A SER* 2.7 33.8 + - - -
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Residues in contact with TYR 564 (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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222A PHE* 3.6 23.6 - + + -
528A THR* 4.0 22.6 - - + +
532A HIS* 4.4 9.0 - - - -
538A PHE* 3.6 30.1 - + + -
560A SER 3.9 1.0 + - - -
561A LEU* 3.2 14.2 + - + +
563A SER* 1.3 77.7 - - - +
565A ILE* 1.3 78.2 + - + +
567A SER* 3.1 14.4 + - - -
568A GLN* 3.4 41.0 + - - +
571A GLU* 4.1 9.4 + - - -
572A PHE* 3.9 20.9 - + - -
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Residues in contact with ILE 565 (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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463A ILE* 4.5 4.9 - - + -
467A GLU* 3.6 9.9 - - - +
525A PHE* 3.6 37.7 - - + +
528A THR* 4.4 14.4 - - + -
529A ILE* 4.4 5.2 - - + -
561A LEU* 3.1 18.9 + - + +
562A TRP* 3.9 20.0 - - + +
564A TYR* 1.3 86.7 - - + +
566A ASN* 1.3 72.8 + - - +
568A GLN 3.1 28.1 + - - +
569A LEU* 3.4 3.9 + - + -
572A PHE* 3.7 30.6 - - + -
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Residues in contact with ASN 566 (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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224A ILE* 3.2 35.2 - - + +
229A VAL* 3.8 18.0 - - - +
463A ILE* 4.1 2.0 - - - +
464A LYS* 4.2 18.3 - - - +
467A GLU* 2.7 41.3 + - - +
562A TRP 2.8 21.0 + - - +
565A ILE* 1.3 75.8 - - - +
567A SER* 1.3 57.6 + - - +
568A GLN 3.1 5.6 + - - -
569A LEU* 3.6 31.3 - - + +
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Residues in contact with SER 567 (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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222A PHE* 3.5 12.9 - - - +
223A PRO* 3.2 39.3 - - - +
224A ILE* 3.6 10.7 + - - +
563A SER 2.7 21.5 + - - -
564A TYR 3.1 6.5 + - - -
566A ASN* 1.3 77.3 - - - +
568A GLN* 1.3 66.5 + - - +
569A LEU 3.8 0.9 - - - -
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Residues in contact with GLN 568 (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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222A PHE* 5.0 5.9 - - - -
564A TYR* 3.4 40.5 + - - +
565A ILE 3.1 6.9 + - - +
567A SER* 1.3 87.8 - - - +
569A LEU* 1.3 64.1 + - - +
570A ASP 3.2 4.3 + - - -
571A GLU* 2.9 42.8 + - + +
572A PHE* 3.5 8.0 - - + -
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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