Contacts of the helix formed by residues 50 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 5.4 0.2 - - + -
9C LEU* 3.8 45.9 - - + +
10C VAL* 4.1 11.9 - - + -
18C LEU* 6.4 0.2 - - + -
25C VAL* 4.3 15.5 - - + -
47C SER 4.6 4.0 + - - +
48C ASN 3.3 0.2 - - - -
49C VAL* 1.3 91.1 - - + +
51C ARG* 1.3 64.8 + - - +
52C ALA* 3.2 2.5 - - - -
53C PHE* 3.0 37.1 + - + +
54C THR* 3.6 7.0 + - - -
130C LEU* 3.8 23.6 - - + -
145C TRP* 4.1 13.7 - - + -
148C VAL* 5.8 1.3 - - + -
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Residues in contact with ARG 51 (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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47C SER 4.6 2.0 + - - -
48C ASN* 3.1 19.7 + - - +
49C VAL 3.4 0.8 + - - -
50C LEU* 1.3 76.7 - - - +
52C ALA* 1.3 55.1 + - - +
54C THR* 2.6 38.0 + - - -
55C PHE* 3.8 10.1 - - + -
77C VAL* 2.9 51.2 + - - +
78C GLY 4.1 2.5 - - - +
79C LEU* 3.9 23.1 - - + +
116C THR* 3.2 32.3 + - - +
203G GLY* 2.8 30.7 + - - +
204G SER 4.0 0.6 + - - -
205G ARG* 3.4 50.6 - - - +
209G ARG* 4.8 2.4 - - - +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C TRP* 4.4 2.6 + - - -
49C VAL 5.7 0.7 - - - +
50C LEU 5.0 1.1 - - - -
51C ARG* 1.3 79.6 - - - +
53C PHE* 1.3 60.3 + - + +
54C THR 3.4 2.6 + - - -
55C PHE* 4.0 16.0 + - - +
78C GLY 3.7 12.2 + - - +
79C LEU* 4.0 11.0 - - + -
124C LEU* 3.7 34.1 - - + +
125C LEU 4.0 16.8 - - - +
126C LEU* 4.5 14.4 - - + -
130C LEU* 5.7 3.6 - - + -
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Residues in contact with PHE 53 (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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10C VAL* 3.7 17.5 - - + +
11C GLU 3.2 21.0 + - - -
14C TRP* 3.3 58.1 - + + +
18C LEU* 4.1 19.1 - - + -
50C LEU* 3.0 35.7 + - + +
51C ARG 2.9 0.2 + - - -
52C ALA* 1.3 76.6 - - + +
54C THR* 1.3 59.1 + - - +
55C PHE 3.4 1.3 - - - -
124C LEU* 5.4 0.9 - - + -
126C LEU* 3.7 27.1 - - + -
130C LEU* 3.8 26.0 - - + -
148C VAL* 4.7 8.7 - - + -
149C THR* 5.0 1.8 - - + -
152C ALA* 3.6 20.0 - - + -
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Residues in contact with THR 54 (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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9C LEU 4.7 6.9 + - - -
10C VAL* 5.2 0.9 - - - +
11C GLU* 3.3 20.3 - - + +
50C LEU 3.6 8.5 + - - -
51C ARG* 2.6 29.9 + - - -
53C PHE* 1.3 71.9 - - - +
55C PHE* 1.3 59.7 + - - +
56C PRO 3.9 0.3 - - - -
100G GLU* 5.2 0.2 - - - +
198G SER* 4.2 8.1 - - - +
202G PHE* 3.7 40.8 - - + +
203G GLY* 3.7 10.8 - - - +
205G ARG* 4.5 8.6 + - - +
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Residues in contact with PHE 55 (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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11C GLU* 4.1 0.4 - - - -
14C TRP* 2.7 32.2 + - - -
51C ARG* 3.8 25.6 - - - -
52C ALA* 4.0 11.1 + - - +
53C PHE 3.4 0.4 - - - -
54C THR* 1.3 78.8 - - - +
56C PRO* 1.3 67.3 - - + +
60C VAL* 5.4 0.5 - - - +
79C LEU* 4.5 4.0 - - + -
116C THR* 4.4 7.6 - - + -
119C ALA* 3.8 37.7 - - + +
120C GLN* 3.6 35.7 - - + -
198G SER 4.8 0.2 - - - -
200G GLY* 4.2 13.0 - - - -
202G PHE 3.7 17.0 - - - -
203G GLY* 3.3 33.2 - - - -
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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