Contacts of the helix formed by residues 546 - 551 (chain A) in PDB entry 1CVU
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 LYS 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A PRO 3.9 9.0 - - - -
543A GLN* 3.0 35.4 + - - +
544A TYR 2.7 10.0 + - - +
545A TRP* 1.3 74.5 - - - +
547A PRO* 1.3 75.8 - - + +
548A SER* 3.6 1.1 - - - +
549A THR* 3.0 31.8 + - - +
550A PHE* 3.3 10.5 - - - -
556A PHE* 4.4 3.1 - - - -
2044B ARG 5.0 5.3 + - - -
2046B GLU* 3.0 41.4 + - + +
2058B ASP* 3.3 19.9 + - - +
2060B THR* 4.0 28.6 + - + +
2061B ARG* 4.3 6.0 - - - +
2062B THR* 5.9 0.4 - - - +
2137B LYS* 4.2 0.2 - - - +
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Residues in contact with PRO 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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546A LYS* 1.3 87.5 - - + +
548A SER* 1.3 63.5 + - - +
550A PHE* 2.9 15.4 + - - +
552A GLY* 2.9 25.0 + - - +
553A GLU* 2.7 33.4 - - + +
556A PHE* 3.9 27.6 - - + -
2058B ASP* 3.7 10.5 - - - +
2060B THR* 4.0 9.9 - - + +
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Residues in contact with SER 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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323A TRP* 5.7 0.7 - - - -
546A LYS* 3.6 3.8 - - - +
547A PRO* 1.3 73.2 - - - +
549A THR* 1.3 62.1 + - - +
550A PHE 3.3 0.7 + - - -
551A GLY* 3.3 11.0 + - - -
552A GLY* 4.1 6.1 - - - +
2046B GLU* 3.0 28.8 + - - -
2047B CYS 5.9 0.4 - - - -
2048B MET* 4.3 25.8 - - - +
2058B ASP* 2.5 42.7 + - - +
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Residues in contact with THR 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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331A THR* 4.1 6.8 - - - +
334A LEU* 3.6 34.2 - - + +
539A ILE* 5.9 0.2 - - + -
544A TYR* 2.6 39.1 + - + +
546A LYS* 3.0 9.7 + - - +
547A PRO 2.9 0.6 + - - -
548A SER* 1.3 78.8 + - - +
550A PHE* 1.3 69.9 + - + +
551A GLY 3.4 0.6 + - - -
2137B LYS* 2.9 42.0 + - + +
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Residues in contact with PHE 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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316A LEU* 4.0 2.1 - - - +
331A THR* 3.5 14.1 - - - +
334A LEU* 4.0 25.8 - - + -
335A ILE* 3.6 20.3 - - + +
539A ILE* 4.4 16.2 - - + -
544A TYR 3.9 16.2 - - - -
545A TRP* 4.1 14.8 - + - -
546A LYS 3.3 19.1 - - - -
547A PRO 2.9 4.4 + - - +
549A THR* 1.3 90.7 - - + +
551A GLY* 1.3 60.8 + - - +
552A GLY 3.3 1.3 - - - -
555A GLY* 3.4 28.7 - - - -
556A PHE* 3.3 35.7 - + - +
559A ILE* 3.5 26.7 - - + -
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Residues in contact with GLY 551 (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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316A LEU* 4.5 4.8 - - - +
319A GLU* 5.2 2.8 - - - +
320A HIS* 2.7 23.5 + - - -
323A TRP* 3.4 29.8 - - - -
331A THR* 3.7 3.6 - - - +
548A SER 3.3 6.8 + - - -
549A THR 3.4 1.2 - - - -
550A PHE* 1.3 78.6 - - - +
552A GLY* 1.3 55.9 + - - +
554A VAL* 5.4 2.3 + - - +
555A GLY 5.0 2.3 + - - -
2048B MET* 3.4 13.4 - - - +
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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