Contacts of the helix formed by residues 517 - 525 (chain l) in PDB entry 5XTD
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 517 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515l SER 3.9 1.2 + - - -
516l PRO* 1.3 79.0 - - - +
518l CYS* 1.3 60.0 + - - +
519l THR* 3.2 30.1 - - + +
520l PHE* 2.9 25.7 + - + +
521l TYR* 3.5 3.9 + - - -
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Residues in contact with CYS 518 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128c VAL* 5.8 1.3 - - - -
132c GLN* 3.8 30.3 - - - -
516l PRO 3.8 1.2 + - - -
517l LEU* 1.3 73.5 - - - +
519l THR* 1.3 59.2 + - + +
521l TYR* 3.0 21.9 + - + +
522l PHE* 2.9 24.6 + - - +
528l PHE* 5.6 4.4 - - - -
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Residues in contact with THR 519 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290l VAL* 5.8 0.3 - - - +
517l LEU* 3.2 29.3 - - + +
518l CYS* 1.3 80.3 - - + +
520l PHE* 1.3 58.8 + - - +
522l PHE* 3.1 12.0 + - - +
523l SER* 2.9 28.9 + - - -
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Residues in contact with PHE 520 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294l THR* 3.6 33.9 - - + -
425l ARG* 5.8 3.4 - - - -
516l PRO* 3.5 22.9 - - + -
517l LEU* 2.9 17.5 + - + +
519l THR* 1.3 80.5 + - - +
521l TYR* 1.3 65.9 + + - +
523l SER* 3.1 6.8 + - - -
524l ASN* 2.9 54.2 + - - +
30p TRP* 4.2 17.7 - + - -
76p HIS* 4.0 13.2 - + - -
77p PRO* 4.1 15.3 - - + -
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Residues in contact with TYR 521 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123c PRO* 6.2 2.5 - - + -
124c VAL* 4.6 26.0 - - + -
516l PRO* 3.3 32.9 - - + +
517l LEU 3.5 2.2 + - - -
518l CYS* 3.0 27.1 + - - +
520l PHE* 1.3 84.9 - + - +
522l PHE* 1.3 63.1 + - - +
524l ASN* 4.6 2.5 - - - -
525l MET* 3.1 32.1 + - + +
528l PHE* 3.9 6.6 - - + -
30p TRP* 4.7 8.3 - + - -
73p TYR 4.5 10.9 + - - -
74p ARG* 5.4 2.4 - - - -
75p GLN 5.5 0.7 + - - -
76p HIS* 5.3 2.5 + - - -
77p PRO* 3.4 35.9 - - + -
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Residues in contact with PHE 522 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132c GLN* 4.7 24.2 - - + -
133c LEU* 5.2 2.7 - - + -
136c PHE* 4.5 25.8 - + + -
287l PHE* 4.0 21.5 - + - -
290l VAL* 4.5 19.3 - - + -
291l CYS* 5.1 2.7 - - - -
518l CYS* 2.9 12.7 + - - +
519l THR* 3.3 14.4 - - - +
520l PHE 3.1 0.2 - - - -
521l TYR* 1.3 80.8 - - - +
523l SER* 1.3 67.4 + - - +
525l MET* 3.2 2.8 + - - +
527l GLY* 3.0 55.2 + - - -
528l PHE* 3.5 27.1 - + + -
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Residues in contact with SER 523 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290l VAL* 3.5 32.1 - - - -
291l CYS* 3.7 14.2 - - - +
293l LEU* 5.3 0.9 - - - -
294l THR* 2.7 35.1 + - - +
295l GLN* 3.1 17.5 + - - -
519l THR 2.9 11.9 + - - -
520l PHE* 3.1 9.7 + - - -
522l PHE* 1.3 83.0 - - - +
524l ASN* 1.3 59.4 + - - +
525l MET 3.4 0.3 + - - -
526l LEU* 3.4 5.7 + - - -
527l GLY 5.0 0.7 - - - +
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Residues in contact with ASN 524 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294l THR* 3.3 17.1 + - - +
295l GLN* 3.2 15.2 + - - +
296l ASN* 5.7 0.8 - - - +
520l PHE* 2.9 38.8 + - + +
521l TYR 4.2 2.2 - - - +
523l SER* 1.3 81.5 + - - +
525l MET* 1.3 60.5 + - - +
526l LEU* 3.2 4.1 + - - +
76p HIS* 4.1 5.1 - - - -
77p PRO* 3.6 31.6 - - + +
78p GLN* 2.8 36.8 + - - +
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Residues in contact with MET 525 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122c THR* 5.4 3.1 - - - -
123c PRO* 3.8 32.8 - - + -
124c VAL* 4.9 9.0 - - + +
129c MET* 5.8 4.7 - - + -
521l TYR* 3.1 26.8 + - + +
522l PHE 3.9 2.5 - - - +
523l SER 3.2 0.4 - - - -
524l ASN* 1.3 77.5 - - - +
526l LEU* 1.3 64.2 + - - +
527l GLY 3.0 3.8 - - - -
528l PHE* 2.9 46.4 + - + +
530l PRO* 4.1 4.2 - - - +
531l SER* 4.7 7.7 + - - +
77p PRO* 3.7 31.6 - - + +
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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