Contacts of the helix formed by residues 522 - 536 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A THR* 6.0 2.7 - - - -
521A PHE* 1.3 82.3 - - - +
523A GLU* 1.3 66.2 + - - +
524A LEU* 3.9 10.1 - - - +
525A PHE* 3.1 32.4 + - - +
526A LEU* 3.6 4.1 + - - +
570A ASP 5.1 0.4 + - - -
571A GLU 3.3 20.2 + - - -
572A PHE* 2.9 19.3 + - - +
573A SER 3.5 13.0 + - - +
574A ASN* 3.8 16.2 - - + +
575A PRO* 5.3 2.4 - - + +
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A TRP* 3.2 28.6 + - + +
512A THR* 5.9 1.7 + - - +
522A ASN* 1.3 76.5 - - - +
524A LEU* 1.3 62.7 + - - +
526A LEU* 3.0 20.0 + - - +
527A ILE* 3.1 22.4 + - + +
597A TRP* 2.9 27.7 + - + +
599A ASN* 2.8 37.5 + - - +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASN* 3.3 12.6 + - - +
523A GLU* 1.3 78.1 + - - +
525A PHE* 1.3 55.2 + - - +
527A ILE* 4.5 15.0 - - + -
528A THR* 2.6 44.3 + - - +
571A GLU* 3.4 44.2 - - + +
572A PHE* 3.8 10.3 - - + -
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Residues in contact with PHE 525 (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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463A ILE* 4.0 13.7 - - + -
466A PHE* 3.5 30.5 - + - -
467A GLU* 3.8 28.9 - - + -
521A PHE* 3.3 37.2 - + + -
522A ASN* 3.1 25.1 + - - +
524A LEU* 1.3 75.8 - - - +
526A LEU* 1.3 61.9 + - + +
528A THR* 3.5 2.6 - - - -
529A ILE* 3.0 47.2 + - + +
565A ILE* 3.6 37.4 - - + +
572A PHE* 3.6 19.3 - - + +
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Residues in contact with LEU 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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466A PHE* 4.3 9.6 - - + -
505A VAL* 3.9 18.3 - - + +
508A VAL* 3.9 15.3 - - + -
509A TRP* 3.7 49.1 - - + +
512A THR* 4.4 4.0 - - + -
521A PHE* 3.5 28.0 - - + -
522A ASN 3.9 10.5 - - - +
523A GLU* 3.0 8.3 + - - +
525A PHE* 1.3 85.2 - - + +
527A ILE* 1.3 60.5 + - - +
529A ILE* 3.3 9.6 + - + +
530A LEU* 3.0 31.7 + - - +
597A TRP* 3.9 6.3 - - + -
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Residues in contact with ILE 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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523A GLU* 3.1 30.9 + - + +
524A LEU* 4.0 13.9 - - + +
526A LEU* 1.3 72.5 - - - +
528A THR* 1.3 60.4 + - - +
530A LEU* 3.2 9.3 + - - +
531A ASP* 2.9 29.4 + - - +
597A TRP* 3.5 21.5 - - + -
599A ASN* 3.9 30.1 - - + +
600A TYR* 4.3 7.0 - - + +
603A ARG* 3.6 36.3 - - - +
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Residues in contact with THR 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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524A LEU* 2.6 37.3 + - - +
525A PHE* 3.5 4.7 - - - -
527A ILE* 1.3 69.7 - - - +
529A ILE* 1.3 67.6 + - - +
531A ASP* 3.1 8.4 + - - +
532A HIS* 3.0 42.9 + - + +
561A LEU* 4.8 0.7 - - + -
564A TYR* 4.0 22.4 - - + +
565A ILE* 4.4 10.5 - - + -
572A PHE* 3.2 21.2 - - + -
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Residues in contact with ILE 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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466A PHE* 4.2 14.6 - - + -
470A VAL* 5.4 1.1 - - + -
501A PHE* 3.9 20.4 - - + -
505A VAL* 4.9 6.1 - - + -
525A PHE* 3.0 52.4 + - + +
526A LEU* 3.4 10.5 - - + +
528A THR* 1.3 75.6 - - - +
530A LEU* 1.3 64.9 + - - +
532A HIS* 3.1 4.0 + - - +
533A LEU* 2.9 21.0 + - - +
541A PHE* 3.7 25.7 - - + -
561A LEU* 4.1 9.9 - - + -
562A TRP* 3.7 26.0 - - + -
565A ILE* 4.4 4.0 - - + -
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Residues in contact with LEU 530 (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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501A PHE* 4.6 3.6 - - + -
502A LEU* 4.0 24.2 - - + -
505A VAL* 3.7 30.5 - - + -
526A LEU 3.0 15.9 + - - +
527A ILE* 3.2 7.2 + - - +
529A ILE* 1.3 75.2 - - - +
531A ASP* 1.3 63.4 + - - +
533A LEU* 3.2 28.8 + - + +
534A TYR* 3.7 15.6 + - + -
597A TRP* 3.6 36.6 - - + -
600A TYR* 4.0 37.0 - - + +
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Residues in contact with ASP 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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150A PRO* 5.8 0.3 - - - +
153A VAL* 4.8 5.4 - - - +
178A ASP* 4.8 6.9 - - - +
527A ILE* 2.9 20.6 + - - +
528A THR* 3.1 10.8 + - - +
530A LEU* 1.3 77.1 - - - +
532A HIS* 1.3 66.9 + - + +
533A LEU 3.1 0.2 - - - -
534A TYR* 3.3 9.4 + - - +
535A SER* 3.1 23.8 + - - -
600A TYR* 4.4 1.7 + - - -
603A ARG* 2.8 44.7 + - - -
604A TRP* 5.5 0.2 - - - -
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Residues in contact with HIS 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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132A PHE* 5.4 2.5 - + - -
150A PRO* 6.4 0.7 - - + -
528A THR* 3.0 41.0 + - + +
529A ILE 3.6 2.9 - - - +
531A ASP* 1.3 82.3 - - + +
533A LEU* 1.3 64.7 + - - +
534A TYR 3.2 0.9 - - - -
535A SER* 2.8 32.9 + - - +
536A CYS* 4.0 6.9 + - - -
537A LEU* 3.8 16.2 + - + +
538A PHE* 3.7 29.6 + + + +
541A PHE* 4.0 11.7 - - - +
561A LEU* 3.8 28.3 - - + -
564A TYR* 4.4 8.7 - - - -
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Residues in contact with LEU 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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481A PHE* 3.4 37.9 - - + -
485A VAL* 4.0 17.3 - - + +
487A HIS* 3.2 28.1 - - - -
501A PHE* 4.0 23.6 - - + -
502A LEU* 4.9 6.7 - - + +
529A ILE 2.9 11.5 + - - +
530A LEU* 3.3 23.8 - - + +
531A ASP 3.1 0.2 - - - -
532A HIS* 1.3 80.5 - - - +
534A TYR* 1.3 80.8 + - + +
536A CYS 4.7 0.9 + - - -
541A PHE* 3.9 22.6 - - + +
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Residues in contact with TYR 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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152A GLY* 3.2 21.2 - - - +
153A VAL* 3.7 24.9 - - + -
177A LYS* 3.3 54.2 + - + +
178A ASP* 4.4 9.2 - - + -
384A LEU* 5.3 2.4 - - - +
485A VAL* 3.4 30.5 - - + -
487A HIS* 4.8 1.2 + - - -
499A PRO* 5.3 4.9 - - - +
502A LEU* 3.7 21.6 - - + +
530A LEU* 3.8 14.6 - - + -
531A ASP* 3.3 5.6 + - - +
533A LEU* 1.3 95.4 - - + +
535A SER* 1.3 63.1 + - - +
536A CYS* 3.3 10.9 + - - -
600A TYR* 3.8 15.9 - - - -
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Residues in contact with SER 535 (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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132A PHE* 3.7 20.8 - - - -
150A PRO* 4.0 24.5 - - - -
152A GLY* 4.1 14.6 + - - -
153A VAL* 4.8 0.4 - - - +
214A PHE* 5.4 1.2 - - - +
531A ASP 3.1 14.3 + - - -
532A HIS* 2.8 33.0 + - - -
533A LEU 3.6 0.6 - - - -
534A TYR* 1.3 77.9 - - - +
536A CYS* 1.3 68.9 + - - +
537A LEU* 3.2 9.4 + - - +
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Residues in contact with CYS 536 (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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132A PHE* 4.9 0.2 - - - -
152A GLY* 5.4 2.9 - - - -
213A LEU* 4.3 22.0 - - + -
214A PHE* 3.9 6.0 - - - +
215A ALA* 2.9 26.2 + - - +
487A HIS* 3.5 46.7 - - - -
488A GLY 5.2 0.7 - - - -
532A HIS 4.0 7.4 + - - -
533A LEU 4.7 0.2 + - - -
534A TYR 3.4 10.4 - - - -
535A SER* 1.3 78.7 + - - +
537A LEU* 1.3 60.8 + - - +
538A PHE 3.2 9.0 - - - +
542A LEU* 4.2 14.8 - - + -
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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