Contacts of the helix formed by residues 526 - 538 (chain A) in PDB entry 5FZ9
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 ALA 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A VAL* 3.8 17.3 - - + -
523A PRO* 3.0 12.2 + - + +
525A TYR* 1.3 84.9 - - + +
527A ALA* 1.3 65.0 + - - +
528A GLU 3.3 2.7 - - - -
529A GLN* 3.2 25.4 + - - +
530A LEU* 3.1 22.0 + - - +
566A VAL* 4.6 1.6 - - + -
567A PRO* 4.0 22.0 - - + -
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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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522A VAL* 5.5 0.9 - - - -
523A PRO 3.8 2.7 + - - -
524A GLY 3.2 15.8 + - - +
525A TYR 3.4 0.8 - - - -
526A ALA* 1.3 78.6 - - - +
528A GLU* 1.3 59.6 + - - +
530A LEU* 3.4 4.3 + - - +
531A GLU* 3.1 32.3 + - - +
584A ARG* 3.6 44.0 - - + +
586A TYR* 3.9 19.9 - - + +
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Residues in contact with GLU 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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525A TYR 5.1 1.0 + - - -
526A ALA 3.3 0.8 - - - -
527A ALA* 1.3 71.8 - - - +
529A GLN* 1.3 66.5 + - - +
531A GLU* 3.8 12.3 - - - +
532A ASN* 3.0 34.1 + - - +
584A ARG* 3.0 39.6 + - - +
617A HIS* 4.2 10.7 + - - -
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Residues in contact with GLN 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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525A TYR* 4.2 13.5 - - - +
526A ALA* 3.2 26.7 + - - +
528A GLU* 1.3 78.6 - - - +
530A LEU* 1.3 62.2 + - - +
532A ASN* 3.3 10.8 + - - +
533A VAL* 3.1 26.2 + - + +
564A HIS 5.1 1.8 + - - +
565A GLU* 3.4 28.3 + - - +
566A VAL* 4.1 14.5 - - + +
567A PRO* 4.4 3.1 - - - +
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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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498A TRP* 4.2 9.2 - - + -
522A VAL* 4.0 14.8 - - + -
526A ALA 3.1 9.5 + - - +
527A ALA 3.6 7.9 - - - +
528A GLU 3.3 0.2 - - - -
529A GLN* 1.3 78.4 - - - +
531A GLU* 1.3 61.7 + - + +
533A VAL* 3.2 4.7 + - - +
534A MET* 2.9 47.4 + - + +
561A LEU* 3.9 33.7 - - + -
566A VAL* 4.2 14.8 - - + +
586A TYR* 3.8 54.3 - - + -
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Residues in contact with GLU 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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500A ILE* 4.5 1.9 - - - +
527A ALA* 3.1 20.3 + - - +
528A GLU* 3.8 18.9 - - - +
529A GLN 3.3 0.4 - - - -
530A LEU* 1.3 80.4 - - + +
532A ASN* 1.3 62.1 + - - +
534A MET* 3.2 6.2 + - + +
535A LYS* 2.8 32.5 + - - +
542A PHE* 3.7 15.9 - - + -
584A ARG* 4.6 7.4 + - - -
586A TYR* 2.5 37.3 + - + +
617A HIS* 5.1 4.3 + - - -
1760A EPE 3.2 28.6 - - - +
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Residues in contact with ASN 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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528A GLU* 3.0 27.3 + - - +
529A GLN* 3.6 8.1 - - - +
531A GLU* 1.3 78.1 - - - +
533A VAL* 1.3 62.6 + - + +
535A LYS* 3.3 12.9 + - - +
536A LYS* 3.2 23.0 + - - +
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Residues in contact with VAL 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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529A GLN* 3.1 16.3 + - + +
530A LEU 3.2 6.5 + - - +
532A ASN* 1.3 75.7 - - + +
534A MET* 1.3 63.4 + - - +
536A LYS* 3.3 6.6 + - - +
537A LEU* 3.2 36.4 + - + +
556A MET* 4.7 5.8 - - - -
560A THR* 4.8 2.5 - - + +
561A LEU* 4.1 17.3 - - + -
564A HIS* 3.8 46.4 - - + +
566A VAL* 4.2 13.0 - - + -
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Residues in contact with MET 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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498A TRP* 4.9 16.4 - - + +
530A LEU* 2.9 39.6 + - + +
531A GLU* 3.6 6.5 - - + +
533A VAL* 1.3 76.0 - - - +
535A LYS* 1.3 58.3 + - - +
537A LEU 3.4 0.3 + - - -
538A ALA* 2.8 35.7 + - - +
541A LEU* 3.7 21.1 - - + -
542A PHE* 3.7 9.4 - - + -
554A THR* 4.1 15.0 - - + +
556A MET* 3.7 38.8 - - + +
561A LEU* 5.2 0.4 - - + -
586A TYR* 6.0 2.0 - - + -
1760A EPE 3.4 29.6 - - - +
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Residues in contact with LYS 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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531A GLU 2.8 16.6 + - - +
532A ASN* 3.6 13.9 - - - +
533A VAL 3.3 0.2 - - - -
534A MET* 1.3 77.4 - - - +
536A LYS* 1.3 62.0 + - - +
539A PRO* 3.5 29.0 - - + +
542A PHE* 3.6 46.1 + - + +
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Residues in contact with LYS 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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532A ASN 3.2 13.5 + - - +
533A VAL* 3.7 9.6 - - - +
534A MET 3.3 0.2 - - - -
535A LYS* 1.3 78.9 - - - +
537A LEU* 1.3 70.5 + - + +
538A ALA 3.7 0.2 + - - -
539A PRO* 4.1 6.1 - - - +
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Residues in contact with LEU 537 (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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93A LEU* 4.0 22.5 - - + +
533A VAL* 3.2 25.2 + - + +
536A LYS* 1.3 88.5 - - + +
538A ALA* 1.3 62.2 + - - +
539A PRO* 3.9 2.7 - - - +
556A MET* 4.3 16.8 - - + -
560A THR* 3.7 30.3 - - + -
564A HIS* 4.7 10.1 - - + +
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.4 26.5 - - + +
534A MET* 2.8 13.9 + - - +
537A LEU* 1.3 81.8 - - - +
539A PRO* 1.3 69.1 - - - +
540A GLU* 3.1 19.0 + - - +
541A LEU* 3.3 31.0 + - + +
542A PHE* 3.7 7.6 - - - -
554A THR* 5.5 0.2 - - + -
556A MET* 5.5 1.1 - - + -
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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