Contacts of the helix formed by residues 2546 - 2551 (chain B) 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 LYS2546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG 4.9 4.9 + - - -
46A GLU* 3.1 41.3 + - + +
58A ASP* 3.3 20.9 + - - +
60A THR* 4.0 27.8 + - - +
61A ARG* 4.3 6.5 - - - +
62A THR* 5.9 1.2 - - - +
2542B PRO 3.9 8.3 - - - -
2543B GLN* 3.0 35.0 + - - +
2544B TYR 2.6 10.2 + - - +
2545B TRP* 1.3 73.2 - - - +
2547B PRO* 1.3 76.4 - - + +
2548B SER* 3.8 1.6 - - - +
2549B THR* 3.0 33.0 + - - +
2550B PHE* 3.4 9.7 - - - -
2556B PHE* 4.4 3.4 - - - -
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Residues in contact with PRO2547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP* 3.6 10.1 - - - +
60A THR* 3.9 11.9 - - + +
2546B LYS* 1.3 87.4 - - + +
2548B SER* 1.3 63.1 + - - +
2550B PHE* 2.9 15.2 + - - +
2552B GLY* 3.0 26.3 + - - +
2553B GLU* 2.8 33.0 - - + +
2556B PHE* 3.9 28.4 - - + -
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Residues in contact with SER2548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.0 28.8 + - - -
47A CYS 5.8 0.2 - - - -
48A MET* 4.3 25.9 - - - +
58A ASP* 2.5 43.7 + - - +
2323B TRP* 5.7 1.4 - - - -
2546B LYS* 3.6 3.3 - - - +
2547B PRO* 1.3 72.3 - - - +
2549B THR* 1.3 62.1 + - - +
2550B PHE 3.3 0.5 + - - -
2551B GLY* 3.4 9.4 + - - -
2552B GLY* 4.2 6.7 - - - +
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Residues in contact with THR2549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LYS* 2.9 43.5 + - + +
2331B THR* 4.0 6.8 + - - +
2334B LEU* 3.6 33.6 - - + +
2544B TYR* 2.6 38.6 + - + +
2546B LYS* 3.0 9.9 + - - +
2547B PRO 2.9 0.2 + - - -
2548B SER* 1.3 80.4 + - - +
2550B PHE* 1.3 69.9 + - + +
2551B GLY 3.5 0.7 + - - -
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Residues in contact with PHE2550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2316B LEU* 3.9 1.9 - - - +
2331B THR* 3.5 12.8 - - - +
2334B LEU* 4.0 26.0 - - + -
2335B ILE* 3.6 21.3 - - + +
2539B ILE* 4.4 16.8 - - + -
2544B TYR 3.9 14.4 - - - -
2545B TRP* 4.0 15.3 - + - -
2546B LYS 3.4 16.2 - - - -
2547B PRO 2.9 5.5 + - - +
2549B THR* 1.3 91.0 - - + +
2551B GLY* 1.3 60.1 + - - +
2552B GLY 3.3 1.6 - - - -
2555B GLY* 3.4 28.4 - - - -
2556B PHE* 3.3 39.3 - + - +
2559B ILE* 3.5 26.7 - - + -
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Residues in contact with GLY2551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET* 3.4 12.8 - - - +
2316B LEU* 4.4 4.9 - - - +
2319B GLU* 5.1 3.1 - - - +
2320B HIS* 2.7 23.9 + - - -
2323B TRP* 3.4 29.4 - - - -
2331B THR* 3.7 3.4 - - - +
2548B SER 3.4 7.0 + - - -
2549B THR 3.5 1.0 - - - -
2550B PHE* 1.3 78.2 - - - +
2552B GLY* 1.3 56.4 + - - +
2554B VAL* 5.3 2.3 + - - +
2555B GLY 5.0 1.9 + - - -
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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