Contacts of the helix formed by residues 48 - 53 (chain H) in PDB entry 2R9R
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 LEU 48 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32H SER* 5.2 0.6 - - - -
33H GLU* 2.8 52.3 + - + +
35H VAL* 3.7 23.3 - - + +
47H GLN* 1.3 73.7 - - - +
49H LYS* 1.3 62.3 + - - +
51H LEU* 3.2 7.5 + - + -
52H ALA* 3.0 25.7 + - + +
65H ARG* 3.6 35.2 - - - +
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H SER* 3.9 21.8 + - - +
47H GLN* 3.4 35.7 - - + +
48H LEU* 1.3 79.8 - - - +
50H THR* 1.3 65.8 + - - +
52H ALA* 3.8 8.4 - - - +
53H GLN* 3.4 19.8 + - - +
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Residues in contact with THR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H THR* 3.3 27.7 + - - +
47H GLN* 3.2 21.3 + - - +
48H LEU 3.1 0.6 - - - -
49H LYS* 1.3 82.0 - - - +
51H LEU* 1.3 60.1 + - + +
53H GLN* 3.5 17.6 + - - +
89H LEU* 5.3 0.4 - - + -
92H TYR* 3.4 41.2 - - + +
93H GLN* 3.9 15.0 - - + +
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Residues in contact with LEU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H VAL* 4.1 33.0 - - + -
37H ILE* 4.3 10.1 - - + -
46H THR* 3.9 26.0 - - + +
47H GLN 3.7 2.9 + - - +
48H LEU* 3.2 6.1 + - + +
50H THR* 1.3 76.7 - - - +
52H ALA* 1.3 58.0 + - - +
53H GLN 2.9 11.0 + - - -
54H PHE 3.2 10.0 + - - -
59H LEU* 3.8 36.6 - - + +
60H GLY* 3.4 14.8 - - - -
65H ARG* 5.0 7.6 - - - +
89H LEU* 4.2 10.8 - - + -
92H TYR* 3.6 33.7 - - + -
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H LEU* 3.0 23.1 + - + +
49H LYS* 4.0 9.6 - - - +
50H THR 3.5 0.2 - - - -
51H LEU* 1.3 76.1 - - - +
53H GLN* 1.3 62.9 + - - +
54H PHE 3.1 2.1 + - - -
55H PRO* 3.2 19.1 - - - +
60H GLY 4.4 13.0 - - - +
65H ARG* 5.8 1.1 - - - +
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Residues in contact with GLN 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H LYS 3.4 9.4 + - - +
50H THR* 3.5 18.6 + - - +
51H LEU 2.9 0.2 - - - -
52H ALA* 1.3 77.3 - - - +
54H PHE* 1.3 82.6 + - + +
55H PRO* 3.4 6.6 - - - +
92H TYR 2.8 29.5 + - - -
93H GLN 5.3 0.4 + - - -
95H GLY* 4.0 15.2 - - - +
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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