Contacts of the helix formed by residues 92 - 97 (chain C) in PDB entry 4RE1
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 PRO 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B GLU* 3.9 17.9 - - + +
241B SER 3.8 18.6 - - - +
242B VAL* 3.5 19.5 - - + -
406B TYR* 3.8 20.0 - - + -
91C LEU* 1.3 93.1 - - + +
93C ALA* 1.3 65.1 + - - +
94C SER* 3.8 17.5 - - - +
95C PHE* 3.0 19.2 + - + +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLU* 5.5 0.6 + - - -
91C LEU 3.5 1.7 + - - -
92C PRO* 1.3 73.4 - - - +
94C SER* 1.3 61.9 + - - +
95C PHE 3.1 0.9 + - - -
96C CYS* 3.8 7.4 + - - +
97C LYS* 3.9 10.6 + - - +
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU* 2.6 29.5 + - - -
404B HIS* 3.3 27.7 - - - -
406B TYR* 2.9 20.4 + - - -
92C PRO* 3.8 1.2 - - - +
93C ALA* 1.3 78.1 - - - +
95C PHE* 1.3 63.6 + - - +
96C CYS 3.1 1.1 + - - -
97C LYS* 3.0 28.1 + - - +
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B VAL* 5.3 0.2 - - + -
272B LEU* 3.8 25.4 - - + -
274B LYS* 2.9 52.3 + - + +
276B TRP* 3.6 7.1 - - - -
391B VAL* 3.4 26.9 - - + -
404B HIS* 4.9 0.7 - - - -
406B TYR* 3.3 29.8 - + + +
86C MET* 3.6 34.8 - - + -
91C LEU* 3.9 27.4 - - + -
92C PRO* 3.0 19.8 + - + +
94C SER* 1.3 79.7 + - - +
96C CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LYS* 4.4 7.2 - - - +
276B TRP* 4.0 5.6 + - - -
393B GLU* 4.4 5.8 - - - +
87C CYS* 2.0 60.6 - - + -
93C ALA 3.8 4.7 + - - +
95C PHE* 1.3 94.7 - - - +
97C LYS* 1.3 57.9 + - - +
98C PRO* 3.5 9.8 - - - +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TRP* 3.9 1.1 - - - -
404B HIS* 3.2 9.4 + - - -
93C ALA 3.9 13.6 + - - +
94C SER* 3.0 21.9 + - - +
96C CYS* 1.3 78.7 - - - +
98C PRO* 1.3 71.4 - - - +
99C PRO* 4.4 0.3 - - - +
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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