Contacts of the helix formed by residues 534 - 543 (chain A) in PDB entry 5I73
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 GLY 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A SER 3.7 1.9 + - - -
533A PRO* 1.3 78.5 - - - +
535A TRP* 1.3 69.2 + - - -
536A PHE* 3.2 4.3 - - - -
537A TRP* 3.3 17.9 + - - +
538A ARG* 3.2 18.9 + - - +
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Residues in contact with TRP 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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534A GLY* 1.3 72.6 - - - -
536A PHE* 1.3 89.4 + + + +
538A ARG* 4.3 7.4 - - - -
539A ILE* 2.9 45.4 + - + +
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Residues in contact with PHE 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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126A ILE* 3.5 32.5 - - + -
127A PHE* 3.9 24.9 - + - -
534A GLY* 3.2 1.7 - - - -
535A TRP* 1.3 106.5 - + + +
537A TRP* 1.3 107.5 + + + +
539A ILE* 3.3 13.1 - - + +
540A CYS* 3.2 26.4 - - - -
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Residues in contact with TRP 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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126A ILE* 4.7 1.8 - - + -
130A ILE* 3.5 37.5 - - + -
131A PRO* 4.2 25.4 - - + -
134A TYR* 4.8 9.6 - + + -
358A TYR* 3.1 48.6 + + - -
362A LEU* 5.7 5.6 - - + -
533A PRO* 4.7 3.8 - - + -
534A GLY* 3.3 25.0 + - - +
535A TRP 3.2 0.2 - - - -
536A PHE* 1.3 111.4 - + + +
538A ARG* 1.3 61.0 + - - +
540A CYS* 3.1 4.8 + - - +
541A TRP* 2.9 61.6 + + + -
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Residues in contact with ARG 538 (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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518A ILE* 4.8 4.5 - - + -
522A CYS* 4.4 18.6 - - - -
533A PRO 5.2 1.1 - - - +
534A GLY 3.2 14.4 + - - +
535A TRP* 3.4 8.0 + - - +
537A TRP* 1.3 79.1 - - - +
539A ILE* 1.3 56.8 + - - +
541A TRP* 3.2 14.9 + - - +
542A VAL* 2.9 37.4 + - + +
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Residues in contact with ILE 539 (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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535A TRP* 2.9 30.5 + - + +
536A PHE* 3.3 17.5 - - + +
538A ARG* 1.3 76.6 - - - +
540A CYS* 1.3 66.6 + - - +
542A VAL* 4.0 7.0 - - + +
543A ALA* 3.5 16.6 + - + +
544A ILE* 3.3 20.1 - - + +
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Residues in contact with CYS 540 (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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126A ILE 4.5 0.4 - - - -
127A PHE* 4.0 22.9 - - - +
131A PRO* 3.6 30.5 - - + -
536A PHE* 3.2 34.3 + - - +
537A TRP* 3.1 11.1 + - - +
538A ARG 3.1 0.6 - - - -
539A ILE* 1.3 83.4 - - - +
541A TRP* 1.3 62.6 + - - +
542A VAL 3.3 0.2 - - - -
544A ILE* 3.2 16.7 + - - -
545A SER* 2.9 32.3 + - - -
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Residues in contact with TRP 541 (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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131A PRO* 3.0 44.0 + - + +
132A LEU* 6.0 0.2 - - + -
134A TYR* 3.4 31.9 - + - -
135A MET* 3.5 17.5 - - + +
509A ALA 4.8 0.5 - - - +
513A SER* 3.0 21.0 + - - +
518A ILE* 3.5 32.1 - - + -
521A PHE* 3.4 28.0 - + - -
522A CYS* 3.9 4.9 - - - -
525A VAL* 5.2 0.2 - - + -
533A PRO* 3.6 32.8 - - + -
537A TRP* 2.9 40.3 + + + +
538A ARG* 3.6 10.3 - - - +
540A CYS* 1.3 76.5 - - - +
542A VAL* 1.3 62.1 + - - +
545A SER* 4.5 5.3 - - - -
546A PRO* 3.8 10.4 - - - +
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Residues in contact with VAL 542 (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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513A SER* 3.5 6.3 - - - +
514A TRP* 3.1 36.3 + - + +
518A ILE* 3.7 31.6 - - + -
538A ARG* 2.9 24.5 + - + +
539A ILE* 4.2 7.4 - - + +
541A TRP* 1.3 79.6 - - - +
543A ALA* 1.3 65.8 + - + +
546A PRO* 3.9 3.7 - - - +
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Residues in contact with ALA 543 (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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514A TRP* 5.4 3.4 - - + -
539A ILE* 3.5 9.6 + - + +
542A VAL* 1.3 87.8 - - + +
544A ILE* 1.3 72.4 + - + +
545A SER 3.4 1.8 - - - -
546A PRO* 3.6 4.3 - - - +
547A LEU* 3.2 40.2 + - + +
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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