Contacts of the helix formed by residues 563 - 577 (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 PRO 563 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558l LEU 3.1 19.7 - - - +
559l GLU* 3.0 28.0 - - - +
562l LEU* 1.3 84.5 - - + +
564l LYS* 1.3 66.9 + - + +
566l ILE* 3.9 0.2 - - - +
567l SER* 2.9 27.4 + - - -
701l PEE 3.9 23.6 - - + +
148r TYR* 3.0 45.8 - - + +
152r TYR* 3.9 9.9 - - + +
214r LEU* 4.6 0.2 - - + -
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Residues in contact with LYS 564 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559l GLU* 2.9 38.3 + - - +
560l LYS* 4.4 2.5 - - - -
563l PRO* 1.3 79.1 - - + +
565l THR* 1.3 61.9 + - + +
567l SER* 2.2 28.3 + - - +
568l GLN* 2.9 27.1 + - - +
701l PEE 5.2 12.7 - - + +
77o TYR* 3.1 42.5 - - + +
144r ASN* 4.5 12.1 - - - +
148r TYR* 4.8 11.9 - - + -
218r LYS* 4.4 14.1 - - - +
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Residues in contact with THR 565 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560l LYS* 2.7 63.0 + - + +
561l LEU* 4.0 10.0 + - - -
564l LYS* 1.3 74.3 - - + +
566l ILE* 1.3 65.1 + - - +
568l GLN* 3.4 14.2 + - - +
569l HIS* 2.9 45.6 + - - -
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Residues in contact with ILE 566 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117V TYR* 3.7 24.2 - - - +
561l LEU 4.6 1.3 - - - +
562l LEU* 3.0 43.2 + - + +
563l PRO 3.4 1.2 + - - +
564l LYS 3.3 0.6 - - - -
565l THR* 1.3 81.8 + - - +
567l SER* 1.3 55.1 + - - +
569l HIS* 2.7 35.4 + - + +
570l GLN* 2.5 41.2 + - - +
701l PEE 4.5 33.0 - - + -
501r PLX 5.9 2.0 - - + -
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Residues in contact with SER 567 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563l PRO 2.9 15.0 + - - -
564l LYS* 2.2 31.5 + - - -
566l ILE* 1.3 77.2 - - - +
568l GLN* 1.3 55.9 + - - +
570l GLN* 2.9 12.6 + - - +
571l ILE* 2.4 37.5 + - - +
701l PEE 3.6 54.8 - - - +
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Residues in contact with GLN 568 (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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564l LYS* 2.9 23.2 + - - +
565l THR* 3.8 15.7 - - - +
567l SER* 1.3 81.8 + - - +
569l HIS* 1.3 60.5 + - - +
571l ILE* 3.6 15.4 - - + +
572l SER* 2.9 30.3 + - - -
701l PEE 5.4 11.2 - - - -
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Residues in contact with HIS 569 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110V ILE* 6.5 0.7 - - + -
113V ALA* 4.8 19.2 - - + +
117V TYR* 4.8 13.4 + + - -
167i TRP* 4.4 2.2 - - + -
565l THR* 2.9 37.0 + - - -
566l ILE* 2.7 34.0 + - + +
568l GLN* 1.3 72.2 - - - +
570l GLN* 1.3 62.2 + - - +
572l SER* 2.8 23.1 + - - -
573l THR* 2.9 15.1 + - - -
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Residues in contact with GLN 570 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167i TRP* 3.0 33.5 - - + -
170i LEU* 3.5 7.0 - - + +
288i LEU* 3.6 26.0 - - + -
566l ILE* 2.5 47.0 + - - +
567l SER* 2.9 11.7 + - - +
569l HIS* 1.3 79.9 - - - +
571l ILE* 1.3 63.1 - - - +
574l SER* 3.1 24.4 + - - -
701l PEE 3.2 46.2 - - + +
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Residues in contact with ILE 571 (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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53Q TYR* 3.7 39.3 - - + -
170i LEU* 4.9 2.7 - - + -
567l SER 2.4 45.6 + - - +
568l GLN* 3.6 15.3 - - + +
569l HIS 3.2 0.2 - - - -
570l GLN* 1.3 76.2 - - - +
572l SER* 1.3 63.8 + - - +
574l SER* 2.5 24.3 + - - -
575l ILE* 3.2 16.1 - - + +
701l PEE 1.6 52.0 - - + +
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Residues in contact with SER 572 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568l GLN 2.9 14.5 + - - -
569l HIS* 2.8 19.1 + - - -
571l ILE* 1.3 77.9 - - - +
573l THR* 1.3 63.5 + - - +
575l ILE* 3.2 12.1 + - - +
576l ILE* 3.2 29.1 + - - +
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Residues in contact with THR 573 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167i TRP* 2.5 47.5 - - - -
569l HIS 2.9 9.5 + - - -
571l ILE 3.4 0.2 - - - -
572l SER* 1.3 77.6 + - - +
574l SER* 1.3 60.7 + - - +
576l ILE* 3.2 28.6 + - - +
577l THR* 3.4 12.5 + - - +
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Residues in contact with SER 574 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q TYR* 4.7 6.4 - - - +
167i TRP* 3.2 28.5 - - - +
168i GLY 5.2 0.3 - - - +
170i LEU* 3.5 23.0 - - - +
171i ASN* 4.8 12.3 + - - +
570l GLN 3.1 13.5 + - - -
571l ILE* 2.5 24.8 + - - -
573l THR* 1.3 74.4 - - - +
575l ILE* 1.3 64.7 + - - +
577l THR* 2.5 21.2 + - - -
578l SER* 3.3 6.1 + - - -
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Residues in contact with ILE 575 (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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53Q TYR* 3.8 32.3 - - + +
54Q PRO 4.9 6.1 - - - +
55Q SER* 4.2 20.9 - - - -
171i ASN* 4.8 4.0 - - - +
571l ILE* 3.2 22.2 - - + +
572l SER* 3.2 13.6 + - - +
574l SER* 1.3 83.2 + - - +
576l ILE* 1.3 59.8 + - + +
578l SER* 2.2 44.7 + - - +
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Residues in contact with ILE 576 (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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201V CDL 3.1 98.0 + - + +
572l SER* 3.2 18.0 + - - +
573l THR* 3.3 18.6 - - - +
574l SER 3.2 0.2 - - - -
575l ILE* 1.3 78.8 - - + +
577l THR* 1.3 58.6 + - + +
578l SER 3.2 8.1 - - - +
579l THR* 5.4 0.2 - - - +
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Residues in contact with THR 577 (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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201V CDL 3.7 36.8 - - + -
164i ALA 5.5 1.6 - - - +
167i TRP* 3.4 29.5 + - + -
168i GLY* 3.5 14.9 + - - +
172i GLN* 6.0 0.3 + - - -
181i TYR* 5.5 2.6 + - - -
97k GLN 5.6 3.5 - - - -
573l THR 3.4 10.3 + - - +
574l SER 2.5 21.7 + - - -
576l ILE* 1.3 78.0 - - + +
578l SER* 1.3 61.4 + - - +
579l THR* 3.8 10.9 - - - +
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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