Contacts of the helix formed by residues 520 - 535 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.3 20.3 - - + +
87B SER* 2.9 26.7 + - - -
467B ARG* 2.8 38.5 + - - +
472B MET* 3.7 11.8 - - - +
475B TYR* 4.4 3.2 + - - +
510B GLU* 3.0 10.1 + - - +
511B LYS 4.5 1.4 + - - -
513B HIS* 3.8 25.1 + - + +
519B GLY* 1.3 69.0 - - - +
521B SER* 1.3 66.8 + - - +
523B ILE* 3.1 5.7 + - - +
524B GLU* 2.9 32.9 + - + +
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Residues in contact with SER 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B PHE* 3.2 20.4 - - - -
467B ARG* 2.8 25.3 + - - -
472B MET* 4.0 9.9 - - - -
507B LEU* 3.7 11.7 - - - -
510B GLU* 2.7 31.5 + - - -
520B GLU* 1.3 72.5 - - - +
522B MET* 1.3 55.9 + - - -
525B MET* 2.8 43.8 + - - +
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Residues in contact with MET 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 3.8 25.8 - - + +
387B TRP* 3.6 31.2 - - + +
434B ILE* 3.7 24.2 - - + -
435B GLY* 5.5 0.4 - - - +
507B LEU* 4.1 26.2 + - + +
508B LEU* 4.3 16.2 - - + -
510B GLU* 4.4 1.0 + - - -
518B PHE* 3.1 44.9 - - + -
519B GLY 3.6 7.0 + - - +
520B GLU 3.1 1.0 + - - -
521B SER* 1.3 76.3 - - - +
523B ILE* 1.3 54.8 + - - +
525B MET* 5.2 0.4 - - - -
526B GLY* 2.8 31.5 + - - -
530B 0AH 4.7 3.1 - - + +
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Residues in contact with ILE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B HIS* 3.9 29.2 - - + +
120B ARG* 3.8 8.2 + - - +
352B LEU 5.8 1.8 - - - +
353B SER* 5.6 3.4 - - - +
355B TYR* 4.3 7.9 - - + +
513B HIS* 4.0 18.6 - - + +
516B SER* 5.7 2.5 - - - +
518B PHE* 3.7 30.1 - - + +
519B GLY 3.7 3.5 + - - +
520B GLU* 3.1 6.6 + - - +
522B MET* 1.3 80.0 - - - +
524B GLU* 1.3 80.0 + - - +
527B ALA* 2.9 36.5 + - - +
711B SAL 4.2 32.1 - - + +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.8 26.5 - - + +
120B ARG* 2.8 29.5 + - - +
123B LEU* 4.5 1.7 - - - +
355B TYR* 5.6 0.2 + - - -
470B PHE* 3.6 21.8 - - - +
472B MET* 3.4 36.1 - - + -
513B HIS* 6.1 0.7 - - + -
520B GLU* 2.9 29.6 + - + +
523B ILE* 1.3 83.5 - - + +
525B MET* 1.3 57.8 + - - +
528B PRO* 3.7 11.4 - - - +
702B BOG 3.4 27.7 + - - +
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Residues in contact with MET 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 3.7 11.4 - - + -
463B PHE* 4.1 11.0 - - + -
466B TYR* 3.8 8.7 - - + -
467B ARG* 3.8 23.6 - - - +
470B PHE* 3.6 36.7 - - + -
472B MET* 3.7 14.6 - - + -
503B PHE* 3.6 29.4 - - + -
507B LEU* 4.0 7.6 - - - -
521B SER* 2.8 38.4 + - - +
524B GLU* 1.3 75.8 - - - +
526B GLY* 1.3 63.1 + - - +
527B ALA 3.7 0.4 - - - -
528B PRO* 3.7 3.5 - - - +
529B PHE* 3.0 27.8 - - + -
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Residues in contact with GLY 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 4.3 0.9 - - - -
384B LEU* 3.5 23.3 - - - +
522B MET 2.8 20.2 + - - -
525B MET* 1.3 78.2 - - - +
527B ALA* 1.3 64.6 + - - +
528B PRO 3.3 0.4 - - - -
529B PHE* 3.0 8.3 + - - +
530B 0AH 2.9 31.3 + - - +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ARG* 4.0 16.4 - - + +
523B ILE 2.9 18.4 + - - +
526B GLY* 1.3 75.2 - - - +
528B PRO* 1.3 59.7 - - + +
530B 0AH 3.2 11.9 + - - +
531B LEU* 2.7 33.3 + - - +
711B SAL 3.5 40.2 - - + +
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Residues in contact with PRO 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 3.3 41.3 - - + +
121B SER* 5.0 0.2 - - - -
123B LEU* 3.8 20.6 - - + -
124B ILE* 3.7 20.9 - - + -
470B PHE* 4.3 4.9 - - + -
523B ILE 3.9 0.2 - - - +
524B GLU 3.7 20.0 - - - +
525B MET 3.7 4.0 - - - +
526B GLY 3.5 4.0 - - - -
527B ALA* 1.3 90.5 - - + +
529B PHE* 1.3 66.8 + - - +
531B LEU 4.5 0.2 - - - +
532B LYS* 2.9 28.5 + - - +
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Residues in contact with PHE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.4 23.1 - - + -
151B ILE* 3.3 42.6 - - + -
375B ASN* 4.7 2.3 + - - +
378B ALA* 3.6 17.5 - - + -
380B GLU* 4.3 10.5 - - + -
381B PHE* 3.2 59.2 - + + -
384B LEU* 4.2 6.7 - - + -
470B PHE* 3.4 16.4 - + - -
503B PHE* 5.7 1.3 - + - -
525B MET* 3.0 25.6 - - + -
526B GLY 3.0 4.1 + - - +
528B PRO* 1.3 80.5 - - - +
530B 0AH 1.3 63.2 + - - +
532B LYS* 4.1 1.2 - - - +
533B GLY* 3.1 18.5 + - - -
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Residues in contact with 0AH 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 5.5 5.4 - - - -
344B VAL* 5.6 1.7 - - - +
348B TYR* 4.9 4.5 - - + -
349B VAL* 4.9 7.1 - - - +
352B LEU* 4.0 10.7 - - + -
381B PHE* 4.1 9.5 - - + -
384B LEU* 5.0 2.2 - - + -
385B TYR* 3.1 49.5 + - + +
387B TRP* 3.9 16.3 - - + -
518B PHE* 5.2 2.4 - - + -
522B MET* 4.7 5.4 - - + +
526B GLY* 2.9 29.5 + - - +
527B ALA* 3.4 9.1 - - - +
529B PHE* 1.3 75.6 + - - +
531B LEU* 1.3 68.4 + - - -
533B GLY* 3.2 4.5 + - - -
534B LEU* 3.1 30.5 + - - +
711B SAL 3.4 38.9 - - + -
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 5.6 3.4 - - + -
116B VAL* 4.0 19.3 - - + -
117B LEU* 4.0 25.1 - - + -
120B ARG* 4.1 15.9 - - + -
121B SER* 4.3 9.2 + - - +
345B ILE* 4.7 16.4 - - + -
349B VAL* 5.2 6.1 - - + -
359B LEU* 6.3 0.9 - - + -
527B ALA 2.7 20.1 + - - +
528B PRO 4.5 0.4 - - - +
530B 0AH 1.3 73.7 - - - -
532B LYS* 1.3 63.7 + - - +
534B LEU* 4.4 17.0 - - + -
535B LEU* 3.1 30.3 + - + +
711B SAL 3.4 37.7 - - + +
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Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 4.1 20.5 + - - +
124B ILE* 4.2 28.4 + - + -
125B PRO 5.6 0.2 - - - -
126B SER* 3.8 26.2 - - - -
371B PHE* 3.7 23.1 - - + -
372B GLN* 3.0 29.2 + - - +
374B ARG 3.1 23.0 + - - -
375B ASN* 3.4 15.7 + - - +
528B PRO 2.9 17.5 + - - +
529B PHE 4.1 1.8 - - - +
531B LEU* 1.3 76.9 - - - +
533B GLY* 1.3 57.8 + - - +
534B LEU 3.0 0.2 - - - -
536B GLY* 2.8 30.1 + - - -
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Residues in contact with GLY 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY* 4.9 3.5 - - - -
228B VAL* 4.2 15.4 + - - +
375B ASN* 3.3 30.7 - - - +
381B PHE* 6.5 0.4 - - - -
529B PHE 3.1 13.7 + - - -
530B 0AH 3.2 5.6 + - - -
532B LYS* 1.3 76.5 - - - +
534B LEU* 1.3 65.9 + - - +
536B GLY* 4.5 1.7 - - - -
537B ASN* 5.2 4.3 - - - +
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Residues in contact with LEU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B PHE* 4.4 7.4 - - + -
228B VAL* 3.9 22.0 - - + -
341B ILE* 3.7 38.3 - - + +
344B VAL* 3.4 33.7 - - + -
345B ILE* 3.6 18.6 - - + -
349B VAL* 5.1 4.0 - - + -
530B 0AH 3.1 20.7 + - - +
531B LEU* 3.8 13.9 - - + +
532B LYS 3.0 0.8 - - - -
533B GLY* 1.3 86.7 - - - +
535B LEU* 1.3 72.0 + - + +
536B GLY 3.4 0.2 - - - -
537B ASN* 3.8 15.1 - - - +
540B CYS* 3.9 2.9 - - - -
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.6 34.3 - - + -
121B SER* 5.8 0.7 - - - +
345B ILE* 4.4 15.0 - - + -
361B PHE* 4.1 20.2 - - + -
362B ASP 5.8 0.7 - - - +
363B PRO* 5.0 9.2 - - + -
366B LEU* 3.8 17.3 - - + -
371B PHE* 3.4 22.2 - - + -
373B TYR* 3.4 7.1 - - - -
531B LEU* 3.1 19.5 + - + +
534B LEU* 1.3 79.4 - - + +
536B GLY* 1.3 58.2 + - - +
537B ASN 2.7 12.9 + - - -
540B CYS* 3.2 40.6 - - + +
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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
------------------------------------------------------------
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