Contacts of the helix formed by residues 50 - 55 (chain M) in PDB entry 2ZHX
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 50 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M LEU* 5.6 1.3 - - + -
9M LEU* 4.0 50.0 - - + +
10M VAL* 4.3 11.0 - - + -
25M VAL* 4.4 14.4 - - + -
46M GLY 5.1 0.2 + - - -
47M SER 4.9 2.9 + - - -
48M ASN 3.4 0.4 - - - -
49M VAL* 1.3 94.3 - - + +
51M ARG* 1.3 57.5 + - - +
52M ALA* 3.2 4.0 - - - +
53M PHE* 2.8 44.9 + - + +
54M THR* 3.8 5.1 + - - -
130M LEU* 3.8 12.1 - - + -
145M TRP* 3.7 20.4 - - + -
148M VAL* 5.5 2.2 - - + -
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Residues in contact with ARG 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M SER 4.6 4.7 + - - +
48M ASN* 2.9 39.3 + - - +
49M VAL 3.2 0.6 - - - -
50M LEU* 1.3 73.6 - - - +
52M ALA* 1.3 67.2 + - - +
54M THR* 2.9 28.1 + - - +
55M PHE* 3.8 18.7 - - + -
77M VAL* 3.1 49.8 + - - +
78M GLY 4.2 2.9 - - - +
79M LEU* 3.9 19.9 - - + +
116M THR* 3.0 41.0 + - - +
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Residues in contact with ALA 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M TRP* 4.3 4.0 + - - -
49M VAL 5.4 1.6 - - - +
50M LEU* 4.7 2.0 - - - -
51M ARG* 1.3 79.6 - - - +
53M PHE* 1.3 67.5 + - + +
54M THR 3.4 2.6 + - - -
55M PHE* 3.8 15.8 + - - +
78M GLY 3.8 6.3 + - - +
79M LEU* 3.7 15.6 - - + +
124M LEU* 3.9 31.0 - - + +
125M LEU 4.1 14.6 - - - +
126M LEU* 4.8 10.8 - - + -
130M LEU* 5.8 3.8 - - + -
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Residues in contact with PHE 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M VAL* 3.6 19.4 - - + +
11M GLU 2.9 22.0 + - - -
14M TRP* 3.2 61.7 - + + +
18M LEU* 3.8 17.9 - - + -
50M LEU* 2.8 32.6 + - + +
52M ALA* 1.3 78.8 - - + +
54M THR* 1.3 61.8 + - - +
55M PHE 3.3 2.2 - - - -
124M LEU* 5.2 0.7 - - + -
126M LEU* 3.8 26.0 - - + -
130M LEU* 3.7 25.1 - - + -
148M VAL* 4.6 9.4 - - + -
149M THR* 5.3 0.7 - - - -
152M ALA* 3.8 15.0 - - + -
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Residues in contact with THR 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M LEU 4.6 8.3 + - - -
10M VAL* 5.0 1.1 - - - -
11M GLU* 3.4 20.9 - - + +
50M LEU 3.8 2.4 + - - -
51M ARG* 2.9 27.7 + - - +
53M PHE* 1.3 79.9 - - - +
55M PHE* 1.3 65.9 + - + +
56M PRO* 3.9 2.8 - - - +
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Residues in contact with PHE 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLU* 4.1 1.1 - - - -
14M TRP* 2.7 33.4 + - - -
51M ARG* 3.8 36.8 - - + -
52M ALA* 3.8 11.3 + - - +
53M PHE 3.3 0.6 - - - -
54M THR* 1.3 84.1 - - + +
56M PRO* 1.3 70.6 - - + +
60M VAL* 5.1 2.7 - - + +
79M LEU* 4.7 3.6 - - + -
116M THR* 4.4 15.0 - - + -
119M ALA* 3.7 35.2 - - + +
120M GLN* 3.5 40.6 - - + -
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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