Contacts of the helix formed by residues 522 - 532 (chain X) in PDB entry 1T6B
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 THR 522 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520X ASP* 4.2 4.5 + - + -
521X MET* 1.3 105.4 - - - +
523X LEU* 1.3 64.2 + - - +
524X LYS* 3.5 6.1 + - - +
525X GLU* 3.1 22.7 + - + +
526X ALA* 3.0 4.0 + - - +
578X LEU 3.9 3.6 - - - -
579X ASP* 3.4 26.6 + - + +
581X ILE 3.1 11.4 - - - +
582X LYS* 4.7 12.1 - - + +
583X LEU* 4.4 1.6 - - - -
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Residues in contact with LEU 523 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491X ILE* 4.5 6.5 - - + -
522X THR* 1.3 71.3 - - - +
524X LYS* 1.3 62.5 + - - +
526X ALA* 3.3 2.4 + - - +
527X LEU* 3.0 38.1 + - + +
552X PHE* 3.8 31.2 - - + -
554X PHE* 5.0 7.2 - - + -
562X ILE* 5.4 0.7 - - + -
574X ILE* 4.3 10.3 - - + -
578X LEU* 3.5 35.2 + - + +
581X ILE* 3.0 30.1 + - + +
583X LEU* 3.8 22.9 - - + +
589X ILE* 4.5 12.8 - - + -
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Residues in contact with LYS 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522X THR* 3.2 5.4 - - - +
523X LEU* 1.3 78.0 - - - +
525X GLU* 1.3 67.1 + - - +
527X LEU* 3.3 4.0 + - - +
528X LYS* 3.1 35.7 + - + +
535X GLU* 3.0 40.2 + - - +
538X GLY 5.7 0.6 + - - -
540X LEU* 3.9 29.8 - - + +
578X LEU* 3.0 32.3 + - + +
579X ASP* 3.6 25.1 - - + +
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Residues in contact with GLU 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X THR* 5.4 8.8 - - - +
218X LYS 5.0 7.3 + - - +
253X HIS* 5.5 1.4 + - - +
255X LEU* 6.4 1.6 - - + -
521X MET* 2.9 23.8 - - + -
522X THR* 3.1 12.4 + - + +
524X LYS* 1.3 80.2 - - - +
526X ALA* 1.3 56.5 + - - +
528X LYS* 3.0 24.6 + - - +
529X ILE* 2.8 52.7 + - + +
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Residues in contact with ALA 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491X ILE* 3.9 5.8 - - + -
505X ILE* 3.9 16.6 - - + -
521X MET* 2.9 16.3 - - + +
522X THR 3.0 12.2 + - - +
523X LEU 3.6 4.7 - - - +
524X LYS 3.2 0.2 - - - -
525X GLU* 1.3 74.3 - - - +
527X LEU* 1.3 60.1 + - - +
529X ILE* 4.1 6.7 - - - -
530X ALA* 2.9 37.3 + - - +
583X LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491X ILE* 3.8 22.4 - - + -
523X LEU* 3.0 26.0 + - + +
524X LYS 3.6 4.0 - - - +
525X GLU 3.3 0.2 - - - -
526X ALA* 1.3 75.7 - - - +
528X LYS* 1.3 64.5 + - - +
531X PHE* 3.2 22.3 + - + -
532X GLY 3.3 5.9 + - - -
533X PHE* 3.3 35.4 + - + -
540X LEU* 4.1 13.0 - - + -
547X ILE* 3.9 25.4 - - + -
552X PHE* 4.0 15.3 - - + -
578X LEU* 4.7 1.6 - - + -
591X ILE* 3.7 22.9 - - + -
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Residues in contact with LYS 528 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524X LYS* 3.1 21.4 + - + +
525X GLU* 3.0 29.8 + - - +
527X LEU* 1.3 77.6 - - - +
529X ILE* 1.3 64.2 + - + +
532X GLY* 2.8 28.6 + - - -
533X PHE 3.1 28.2 - - - +
534X ASN* 4.6 6.3 - - - +
535X GLU* 2.6 34.1 + - - +
540X LEU* 3.8 17.9 - - + -
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Residues in contact with ILE 529 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217X THR* 5.8 6.5 - - + -
250X GLU* 3.5 21.5 - - - +
253X HIS* 3.7 44.7 - - + +
255X LEU* 4.1 13.0 - - + -
256X VAL* 3.7 24.3 - - + +
505X ILE* 4.2 11.2 - - + -
521X MET* 4.7 7.6 - - + -
525X GLU* 2.8 43.5 + - + +
526X ALA* 3.8 6.7 - - - +
528X LYS* 1.3 79.0 - - + +
530X ALA* 1.3 61.5 + - + +
532X GLY 4.9 0.3 + - - -
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Residues in contact with ALA 530 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X GLU* 3.8 11.6 - - - +
256X VAL* 4.3 11.0 - - + -
503X ARG* 3.6 39.8 + - + +
505X ILE* 3.9 27.1 - - + -
526X ALA 2.9 19.4 + - - +
529X ILE* 1.3 78.1 - - - +
531X PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 531 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491X ILE* 3.5 39.3 - - + -
493X PHE* 3.5 40.8 - + + -
501X VAL* 3.6 29.4 - - + -
503X ARG* 3.5 30.5 - - + -
527X LEU* 3.2 23.9 + - + +
530X ALA* 1.3 86.1 - - + +
532X GLY* 1.3 63.9 + - - +
533X PHE* 3.9 13.9 - + + -
542X TYR* 3.5 18.7 - + - -
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Residues in contact with GLY 532 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527X LEU 3.3 0.2 + - - -
528X LYS 2.8 16.5 + - - -
529X ILE 4.7 0.4 + - - -
531X PHE* 1.3 79.5 - - - +
533X PHE* 1.3 67.9 + - - +
534X ASN* 3.5 9.7 + - - +
541X GLN 4.3 0.2 - - - +
542X TYR* 4.5 8.0 - - - -
543X GLN 5.8 0.2 + - - -
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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