Contacts of the helix formed by residues 545 - 553 (chain A) in PDB entry 5VLR
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 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A LEU* 3.9 20.9 - - + -
538A VAL* 3.9 5.8 - - + +
542A PHE* 2.9 30.2 + - + +
544A GLU* 1.4 76.7 - - - +
546A LEU* 1.4 57.1 + - - +
547A ALA 3.3 2.5 - - - +
548A ARG* 3.2 25.4 + - - +
549A LEU* 3.0 25.8 + - - +
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Residues in contact with LEU 546 (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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543A PRO 3.3 16.1 + - - +
544A GLU 3.3 1.8 - - - -
545A ALA* 1.4 72.9 - - - +
547A ALA* 1.3 59.6 + - - +
549A LEU* 3.2 2.6 + - + -
550A LEU* 2.9 55.7 + - + +
564A MET* 4.8 5.6 - - - -
568A LEU* 3.9 24.9 - - + -
571A TRP* 3.6 45.3 - - + -
574A LEU* 4.1 9.2 - - + -
582A LEU* 4.3 8.3 - - + -
592A VAL* 6.2 0.4 - - + -
595A PHE* 3.7 32.3 - - + -
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Residues in contact with ALA 547 (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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544A GLU 4.6 5.4 + - - +
545A ALA* 3.3 1.0 - - - -
546A LEU* 1.3 78.1 - - - +
548A ARG* 1.4 62.8 + - + +
550A LEU 3.2 9.9 + - - -
551A LEU* 3.2 23.3 + - + +
574A LEU* 5.8 0.4 - - - +
581A GLU* 3.6 33.9 - - + +
582A LEU* 3.9 13.5 - - + +
587A PHE* 3.6 25.0 - - + -
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Residues in contact with ARG 548 (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 ILE 5.0 3.0 + - - -
515A LEU* 3.7 44.7 - - + +
516A GLU 5.3 0.6 - - - +
521A GLY* 5.2 12.7 - - - +
523A LEU* 5.5 13.1 - - + +
531A VAL* 4.9 2.2 - - + -
544A GLU 5.6 0.2 - - - -
545A ALA* 3.2 22.5 + - - +
547A ALA* 1.4 78.9 - - + +
549A LEU* 1.4 62.7 + - - +
551A LEU* 3.4 11.4 + - + +
552A VAL* 3.3 28.3 + - + +
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Residues in contact with LEU 549 (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 VAL* 3.9 15.2 - - + +
532A TRP* 4.2 3.8 - - + -
535A ARG* 3.7 41.5 - - + +
538A VAL* 4.2 9.6 - - + -
545A ALA 3.0 13.6 + - - +
546A LEU* 3.2 9.2 + - - +
548A ARG* 1.4 76.2 - - - +
550A LEU* 1.3 54.2 + - - +
552A VAL* 3.2 29.9 - - + +
553A THR* 2.7 23.2 + - - -
564A MET* 3.1 27.8 - - + -
567A LEU* 4.6 3.1 - - + -
571A TRP* 3.7 31.2 - - + -
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Residues in contact with LEU 550 (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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546A LEU* 2.9 38.8 + - + +
547A ALA 3.2 4.2 + - - +
549A LEU* 1.3 74.2 - - - +
551A LEU* 1.3 56.5 + - - +
553A THR* 3.5 6.5 - - - -
555A TRP* 2.8 44.1 + - + -
564A MET* 3.7 30.1 - - + -
568A LEU* 4.9 7.2 - - + -
582A LEU* 3.8 26.2 - - + -
587A PHE* 3.8 18.6 - - + -
592A VAL* 3.8 30.5 - - + -
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A GLU* 4.7 14.9 - - + +
521A GLY 5.0 11.9 - - - +
528A LYS* 4.0 17.6 + - - -
547A ALA* 3.2 21.8 + - + +
548A ARG* 3.9 8.3 - - + +
549A LEU 3.3 0.4 - - - -
550A LEU* 1.3 75.7 - - - +
552A VAL* 1.4 64.1 + - + +
553A THR 4.1 4.6 - - - +
555A TRP* 4.9 2.1 + - - +
581A GLU* 5.6 2.0 - - - +
586A SER* 4.1 34.3 - - - +
587A PHE* 4.1 18.8 - - + -
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Residues in contact with VAL 552 (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 LEU* 4.9 11.0 - - + -
528A LYS* 3.6 56.2 + - + +
531A VAL* 3.8 21.1 - - + -
532A TRP* 4.0 14.3 - - + +
548A ARG* 3.3 14.1 + - + +
549A LEU* 3.2 32.5 - - + +
551A LEU* 1.4 77.0 - - + +
553A THR* 1.4 62.8 + - - +
554A LYS* 3.7 9.0 + - - +
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Residues in contact with THR 553 (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 TRP* 3.5 27.1 - - + -
549A LEU 2.7 17.8 + - - -
550A LEU* 3.5 11.9 + - - -
551A LEU 4.1 4.0 - - - +
552A VAL* 1.4 76.4 - - - +
554A LYS* 1.3 63.3 + - - +
555A TRP* 3.1 38.6 + - + -
560A ASP 3.8 13.2 - - - +
561A VAL* 4.6 1.3 - - - +
564A MET* 3.0 33.2 - - + +
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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