Contacts of the helix formed by residues 520 - 535 (chain A) in PDB entry 1PTH
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 GLU 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 3.3 20.6 - - + +
87A SER* 2.9 27.0 + - - -
467A ARG* 2.8 38.2 + - - +
472A MET* 3.7 11.9 - - - +
475A TYR* 4.4 2.5 + - - +
510A GLU* 3.0 10.5 + - - +
511A LYS 4.5 1.4 + - - -
513A HIS* 3.8 24.7 + - + +
519A GLY* 1.3 69.2 - - - +
521A SER* 1.3 66.8 + - - +
523A ILE* 3.1 5.9 + - - +
524A GLU* 2.9 33.3 + - + +
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A PHE* 3.2 20.4 - - - -
467A ARG* 2.8 25.1 + - - -
472A MET* 4.0 10.1 - - - -
507A LEU* 3.7 11.6 - - - +
510A GLU* 2.7 30.6 + - - -
520A GLU* 1.3 73.0 - - - +
522A MET* 1.3 55.8 + - - -
525A MET* 2.8 44.0 + - - +
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Residues in contact with MET 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 3.8 25.8 - - + +
387A TRP* 3.6 31.0 - - + +
434A ILE* 3.7 23.6 - - + -
435A GLY* 5.5 0.7 - - - +
507A LEU* 4.1 26.0 + - + +
508A LEU* 4.3 16.6 - - + -
510A GLU* 4.4 1.4 + - - -
518A PHE* 3.1 45.8 - - + -
519A GLY 3.6 7.0 + - - +
520A GLU 3.1 0.8 + - - -
521A SER* 1.3 76.5 - - - +
523A ILE* 1.3 55.2 + - - +
525A MET* 5.2 0.2 - - - -
526A GLY* 2.8 31.5 + - - -
530A 0AH 4.7 3.4 - - + +
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Residues in contact with ILE 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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90A HIS* 3.9 28.7 - - + +
120A ARG* 3.9 8.1 - - - +
352A LEU 5.8 2.0 - - - +
353A SER* 5.7 3.6 - - - +
355A TYR* 4.3 8.5 - - + +
513A HIS* 4.0 17.9 - - + +
516A SER* 5.7 2.2 - - - +
518A PHE* 3.7 28.5 - - + +
519A GLY 3.7 4.9 + - - +
520A GLU* 3.1 7.7 + - - +
522A MET* 1.3 78.8 - - - +
524A GLU* 1.3 81.4 + - - +
527A ALA* 2.9 35.7 + - - +
710A SAL 4.2 31.0 - - + +
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Residues in contact with GLU 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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86A PRO* 3.8 25.7 - - + +
120A ARG* 2.8 28.4 + - - +
123A LEU* 4.5 1.6 - - - +
355A TYR* 5.6 0.2 + - - -
470A PHE* 3.6 21.8 - - - +
472A MET* 3.4 36.3 - - + -
513A HIS* 6.1 0.7 - - - -
520A GLU* 2.9 30.0 + - + +
523A ILE* 1.3 83.3 - - + +
525A MET* 1.3 59.0 + - - +
528A PRO* 3.7 11.3 - - - +
702A BOG 3.4 27.8 + - - +
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Residues in contact with MET 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 3.7 10.5 - - + -
463A PHE* 4.1 11.0 - - + -
466A TYR* 3.8 9.0 - - + -
467A ARG* 3.8 24.0 - - - +
470A PHE* 3.6 35.8 - - + -
472A MET* 3.7 14.8 - - + -
503A PHE* 3.6 28.5 - - + -
507A LEU* 4.0 7.9 - - - -
521A SER* 2.8 37.2 + - - +
524A GLU* 1.3 76.3 - - - +
526A GLY* 1.3 62.5 + - - +
527A ALA 3.7 0.4 - - - -
528A PRO* 3.7 4.3 - - - +
529A PHE* 3.0 27.8 - - + -
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Residues in contact with GLY 526 (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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381A PHE* 4.3 1.7 - - - -
384A LEU* 3.5 22.8 - - - +
522A MET 2.8 20.4 + - - -
525A MET* 1.3 78.5 - - - +
527A ALA* 1.3 65.5 + - - +
528A PRO 3.3 0.4 - - - -
529A PHE* 3.1 8.1 + - - +
530A 0AH 2.9 30.3 + - - +
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Residues in contact with ALA 527 (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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120A ARG* 4.0 15.7 - - + +
523A ILE 2.9 19.0 + - - +
526A GLY* 1.3 74.3 - - - +
528A PRO* 1.3 60.3 - - + +
530A 0AH 3.2 11.9 + - - +
531A LEU* 2.7 33.1 + - - +
710A SAL 3.5 40.2 - - + +
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Residues in contact with PRO 528 (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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120A ARG* 3.3 43.5 - - + +
121A SER* 5.0 0.2 - - - -
123A LEU* 3.8 21.3 - - + -
124A ILE* 3.7 21.8 - - + -
470A PHE* 4.3 5.2 - - + -
523A ILE 3.9 0.2 - - - +
524A GLU 3.7 18.4 - - - +
525A MET 3.7 4.0 - - - +
526A GLY 3.5 4.3 - - - -
527A ALA* 1.3 88.5 - - + +
529A PHE* 1.3 66.3 + - - +
531A LEU 4.5 0.2 - - - +
532A LYS* 2.9 28.8 + - - +
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Residues in contact with PHE 529 (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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124A ILE* 3.4 22.9 - - + -
151A ILE* 3.3 44.4 - - + -
375A ASN* 4.7 2.4 + - - +
378A ALA* 3.6 17.3 - - + -
380A GLU* 4.3 9.6 - - + -
381A PHE* 3.2 59.2 - + + -
384A LEU* 4.2 6.1 - - + -
470A PHE* 3.4 16.6 - + - -
503A PHE* 5.7 1.6 - + - -
525A MET* 3.0 25.8 - - + -
526A GLY 3.1 3.7 + - - +
528A PRO* 1.3 81.4 - - - +
530A 0AH 1.3 62.7 + - - +
532A LYS* 4.1 1.6 - - - +
533A GLY* 3.1 18.2 + - - -
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Residues in contact with 0AH 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 5.5 5.9 - - - -
344A VAL* 5.6 1.9 - - - +
348A TYR* 4.9 4.9 - - + -
349A VAL* 4.9 6.7 - - - +
352A LEU* 4.0 10.5 - - + -
381A PHE* 4.1 9.8 - - + -
384A LEU* 5.0 2.0 - - + -
385A TYR* 3.1 48.9 + - + +
387A TRP* 3.9 16.1 - - + -
518A PHE* 5.2 2.8 - - + -
522A MET* 4.7 5.2 - - + +
526A GLY* 2.9 29.5 + - - +
527A ALA* 3.4 8.4 - - - +
529A PHE* 1.3 76.2 + - - +
531A LEU* 1.3 68.5 + - - -
533A GLY* 3.2 4.9 + - - -
534A LEU* 3.1 31.7 + - - +
710A SAL 3.4 38.8 - - + -
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Residues in contact with LEU 531 (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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113A MET* 5.6 2.5 - - + -
116A VAL* 4.0 18.6 - - + -
117A LEU* 4.0 24.9 - - + -
120A ARG* 4.2 16.6 - - + -
121A SER* 4.3 9.6 + - - +
345A ILE* 4.7 16.2 - - + -
349A VAL* 5.2 6.7 - - + -
359A LEU* 6.3 1.1 - - + -
527A ALA 2.7 18.8 + - - +
528A PRO* 4.5 0.9 - - + +
530A 0AH 1.3 75.0 - - - -
532A LYS* 1.3 63.4 + - - +
534A LEU* 4.4 15.5 - - + -
535A LEU* 3.1 29.7 + - + +
710A SAL 3.4 37.2 - - + +
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Residues in contact with LYS 532 (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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121A SER* 4.1 20.0 + - - +
124A ILE* 4.2 28.8 + - + +
125A PRO 5.6 0.2 - - - -
126A SER* 3.8 25.6 - - - -
371A PHE* 3.7 23.8 - - + -
372A GLN* 3.0 29.8 + - - +
374A ARG 3.1 22.8 + - - -
375A ASN* 3.4 16.2 + - - +
528A PRO 2.9 17.3 + - - +
529A PHE 4.1 1.3 - - - +
531A LEU* 1.3 76.7 - - - +
533A GLY* 1.3 58.8 + - - +
534A LEU 3.0 0.2 - - - -
536A GLY* 2.8 30.3 + - - -
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Residues in contact with GLY 533 (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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227A GLY* 4.9 3.6 - - - -
228A VAL* 4.2 15.4 + - - +
375A ASN* 3.3 30.6 - - - +
381A PHE* 6.5 0.2 - - - -
529A PHE 3.1 14.8 + - - -
530A 0AH 3.2 5.4 + - - -
532A LYS* 1.3 75.7 - - - +
534A LEU* 1.3 65.9 + - - +
536A GLY* 4.5 2.3 - - - -
537A ASN* 5.2 4.5 - - - +
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Residues in contact with LEU 534 (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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205A PHE* 4.4 7.2 - - + -
228A VAL* 3.9 20.6 - - + -
341A ILE* 3.7 39.8 - - + +
344A VAL* 3.4 33.4 - - + -
345A ILE* 3.6 18.4 - - + -
349A VAL* 5.1 4.5 - - + -
530A 0AH 3.1 21.3 + - - +
531A LEU* 3.8 13.2 - - + +
532A LYS 3.0 0.8 - - - -
533A GLY* 1.3 85.4 - - - +
535A LEU* 1.3 71.9 + - + +
536A GLY 3.4 0.4 - - - -
537A ASN* 3.8 14.4 - - - +
540A CYS* 3.9 3.3 - - - -
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.6 34.8 - - + -
121A SER* 5.8 0.2 - - - +
345A ILE* 4.4 15.0 - - + -
361A PHE* 4.1 19.7 - - + -
362A ASP 5.8 0.9 - - - +
363A PRO* 5.0 8.7 - - + -
366A LEU* 3.8 17.9 - - + -
371A PHE* 3.4 23.1 - - + -
373A TYR* 3.4 7.1 - - - -
531A LEU* 3.1 18.8 + - + +
534A LEU* 1.3 78.8 - - + +
536A GLY* 1.3 57.6 + - - +
537A ASN 2.7 12.7 + - - -
540A CYS* 3.2 40.0 - - + +
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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
------------------------------------------------------------
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