Contacts of the helix formed by residues 522 - 536 (chain B) in PDB entry 5C16
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 ASN 522 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B THR* 5.9 2.5 - - - -
521B PHE* 1.3 86.3 - - - +
523B GLU* 1.3 65.8 + - - +
524B LEU* 3.0 10.9 + - - +
525B PHE* 2.9 36.9 + - - +
526B LEU* 3.5 4.7 + - - +
570B ASP 5.0 0.2 + - - -
571B GLU 3.0 24.0 + - - -
572B PHE* 3.2 8.3 + - - -
573B SER 3.3 22.9 + - - +
574B ASN* 4.3 6.5 - - + +
575B PRO* 5.4 2.4 - - + +
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B TRP* 3.3 26.2 + - + +
512B THR* 5.8 1.5 + - - +
522B ASN* 1.3 72.7 - - - +
524B LEU* 1.3 61.3 + - - +
526B LEU* 3.0 9.9 + - - +
527B ILE* 2.9 36.9 + - + +
597B TRP* 3.1 30.1 + - + +
599B ASN* 2.9 41.2 + - - +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ASN* 3.0 12.8 + - - +
523B GLU* 1.3 78.5 + - - +
525B PHE* 1.3 51.9 + - - +
527B ILE* 3.3 15.4 + - + -
528B THR* 2.7 54.1 + - - +
571B GLU* 3.7 42.0 - - + +
572B PHE* 4.0 5.4 - - + -
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Residues in contact with PHE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ILE* 4.3 11.0 - - + -
466B PHE* 3.8 22.0 - + - -
467B GLU* 4.2 20.2 - - + -
521B PHE* 3.4 41.1 - + + -
522B ASN* 2.9 22.1 + - - +
524B LEU* 1.3 76.8 - - - +
526B LEU* 1.3 61.8 + - + +
528B THR* 3.4 2.4 + - - -
529B ILE* 3.0 56.6 + - + +
562B TRP* 4.6 3.6 - + - -
565B ILE* 3.8 33.2 - - + +
572B PHE* 3.6 23.0 - + + -
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 4.3 10.3 - - + -
505B VAL* 4.0 15.8 - - + +
508B VAL* 3.9 20.4 - - + -
509B TRP* 4.0 30.1 - - + +
512B THR* 4.1 5.6 - - + -
521B PHE* 3.5 35.9 - - + -
522B ASN 4.0 6.1 - - - +
523B GLU* 3.0 8.5 + - - +
525B PHE* 1.3 86.0 - - + +
527B ILE* 1.3 66.6 + - - +
529B ILE* 3.3 8.5 + - + +
530B LEU* 3.1 26.3 + - - +
597B TRP* 3.8 16.2 - - + -
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Residues in contact with ILE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B GLU* 2.9 35.5 + - + +
524B LEU* 3.7 14.8 - - + +
526B LEU* 1.3 75.8 - - - +
528B THR* 1.3 56.7 + - - +
530B LEU* 3.3 6.8 + - - +
531B ASP* 2.9 29.3 + - - +
597B TRP* 3.8 15.7 - - + -
599B ASN* 3.7 29.4 - - + +
600B TYR* 4.2 11.2 - - + +
603B ARG* 3.5 34.8 - - - +
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Residues in contact with THR 528 (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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524B LEU* 2.7 37.3 + - - +
525B PHE 3.7 4.5 - - - -
527B ILE* 1.3 71.2 - - - +
529B ILE* 1.3 67.2 + - - +
531B ASP* 3.2 8.6 + - + +
532B HIS* 3.2 43.8 + - + +
561B LEU* 4.9 0.4 - - + -
564B TYR* 3.9 22.2 - - + +
565B ILE* 4.1 13.2 - - + -
572B PHE* 3.5 17.0 - - + -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 4.3 13.9 - - + -
470B VAL* 5.9 0.7 - - + -
501B PHE* 3.9 20.2 - - + -
505B VAL* 4.9 6.3 - - + -
525B PHE* 3.0 54.1 + - + +
526B LEU* 3.3 13.4 + - + +
528B THR* 1.3 77.8 - - - +
530B LEU* 1.3 57.5 + - - +
532B HIS* 3.5 1.4 + - - +
533B LEU* 3.0 25.5 + - - +
541B PHE* 3.9 26.3 - - + -
561B LEU* 4.2 8.5 - - + -
562B TRP* 4.0 25.6 - - + -
565B ILE* 5.7 2.0 - - + -
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B PHE* 4.4 4.5 - - + -
502B LEU* 4.1 22.2 - - + -
505B VAL* 3.9 39.9 - - + -
526B LEU 3.1 12.5 + - - +
527B ILE 3.6 7.4 - - - +
528B THR 3.2 0.2 - - - -
529B ILE* 1.3 74.1 - - - +
531B ASP* 1.3 65.8 + - - +
532B HIS 3.2 1.7 + - - -
533B LEU* 3.6 27.3 - - + +
534B TYR* 3.2 24.7 - - + -
597B TRP* 3.9 18.6 - - + -
600B TYR* 3.9 34.9 + - + +
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Residues in contact with ASP 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 5.7 1.4 - - + +
153B VAL* 5.6 2.1 - - - +
178B ASP* 4.7 6.3 - - - +
527B ILE* 2.9 23.4 + - - +
528B THR* 3.2 10.0 + - + +
530B LEU* 1.3 81.1 - - - +
532B HIS* 1.3 68.6 + - + +
534B TYR* 3.4 7.7 + - - +
535B SER* 3.2 22.5 + - - -
600B TYR* 4.4 1.4 + - - -
603B ARG* 2.7 45.6 + - - -
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Residues in contact with HIS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 5.4 3.4 - + - -
150B PRO* 6.3 1.3 - - + -
528B THR* 3.2 41.6 + - + +
529B ILE 3.8 3.1 - - - +
530B LEU 3.2 0.2 - - - -
531B ASP* 1.3 81.4 - - + +
533B LEU* 1.3 63.5 + - - +
534B TYR 3.1 2.3 + - - -
535B SER* 2.9 36.8 + - - +
536B CYS* 3.7 6.2 + - - -
537B LEU* 4.1 13.6 + - + +
538B PHE* 3.7 29.5 + + + +
541B PHE* 4.3 8.7 - - + +
561B LEU* 3.8 25.6 - - + -
564B TYR* 4.3 9.1 - + - -
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B PHE* 4.0 23.1 - - + -
485B VAL* 3.8 23.9 - - + +
487B HIS* 3.0 27.1 + - + -
501B PHE* 4.0 19.3 - - + -
502B LEU* 4.9 7.4 - - + +
529B ILE 3.0 17.3 + - - +
530B LEU* 3.6 28.0 - - + +
532B HIS* 1.3 75.6 - - - +
534B TYR* 1.3 83.6 + - + +
536B CYS 4.8 0.3 + - - -
541B PHE* 3.7 24.0 - - + +
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Residues in contact with TYR 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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152B GLY* 2.9 32.5 - - - +
153B VAL* 4.1 22.0 - - + -
177B LYS* 3.6 39.5 + - + +
178B ASP* 4.8 3.6 - - + -
384B LEU* 5.5 1.9 - - - +
485B VAL* 3.4 32.1 - - + -
487B HIS* 4.6 1.0 + - - -
499B PRO* 5.3 4.9 - - - +
502B LEU* 3.6 22.9 - - + +
530B LEU* 3.2 24.5 - - + -
531B ASP* 3.4 6.7 + - - +
532B HIS 3.1 0.4 - - - -
533B LEU* 1.3 94.9 - - + +
535B SER* 1.3 62.6 + - - +
536B CYS* 3.3 11.0 + - - -
600B TYR* 3.8 18.2 - - - -
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Residues in contact with SER 535 (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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132B PHE* 3.8 20.4 - - - -
150B PRO* 4.1 26.9 - - - -
152B GLY* 4.4 11.0 + - - -
153B VAL* 6.0 0.2 - - - -
214B PHE* 5.3 1.6 - - - +
531B ASP 3.2 14.6 + - - -
532B HIS* 2.9 34.5 + - - +
534B TYR* 1.3 76.2 - - - +
536B CYS* 1.3 73.1 + - - +
537B LEU* 3.1 11.0 + - - +
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Residues in contact with CYS 536 (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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132B PHE* 5.0 0.7 - - - -
152B GLY* 5.3 4.9 - - - -
213B LEU* 4.3 18.4 - - + -
214B PHE* 3.8 5.9 + - + +
215B ALA* 2.9 26.7 + - - +
487B HIS* 3.3 47.3 - - - -
488B GLY 5.1 1.6 - - - -
532B HIS 3.7 6.0 + - - -
534B TYR 3.3 9.3 - - - -
535B SER* 1.3 80.1 + - - +
537B LEU* 1.3 59.8 + - - +
538B PHE 3.3 11.7 - - - -
542B LEU* 4.0 14.1 - - + -
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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