Contacts of the helix formed by residues 193 - 198 (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 SER 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C SER* 3.4 10.5 + - - -
191C HIS* 2.7 28.9 + - - +
192C PRO* 1.3 69.8 - - - +
194C PRO* 1.3 67.8 - - - +
195C LEU* 3.9 6.3 + - - +
196C SER* 2.9 10.9 + - - -
197C ALA 2.7 31.5 + - - -
20D GLU* 3.9 5.4 + - - -
22D ILE* 4.0 12.3 - - - +
24D MET* 4.8 4.9 - - - -
43D VAL* 4.1 13.3 - - - +
45D THR* 4.0 8.0 + - - -
56D MET* 5.3 0.2 - - - -
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Residues in contact with PRO 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ARG* 3.7 15.7 - - + -
93C SER 4.1 12.6 - - - +
96C ASN* 3.5 20.9 - - - +
192C PRO 3.4 0.6 - - - +
193C SER* 1.3 88.9 - - - +
195C LEU* 1.3 62.6 + - - +
196C SER 3.3 0.5 + - - -
197C ALA* 3.5 8.7 + - + +
198C SER* 4.6 5.9 + - - -
20D GLU* 4.3 4.0 - - - +
45D THR* 4.0 10.3 - - + -
54D ASN* 3.3 31.2 - - - +
56D MET* 3.7 13.5 - - - -
73D GLN* 3.1 24.7 + - - +
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Residues in contact with LEU 195 (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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193C SER* 3.0 4.2 + - - +
194C PRO* 1.3 78.6 - - - +
196C SER* 1.3 57.3 + - - +
198C SER* 5.4 1.2 + - - -
199C ARG* 4.0 2.9 - - - +
24D MET* 4.2 11.2 - - + -
28D GLU 5.3 0.4 - - - +
29D VAL* 4.4 17.7 - - + -
32D VAL* 3.4 42.6 - - + +
33D ILE* 4.2 9.9 - - + -
43D VAL* 4.0 24.2 - - + -
56D MET* 3.7 15.2 - - - -
58D LEU* 3.8 35.2 - - + -
71D VAL* 4.3 22.9 - - + -
73D GLN* 4.6 3.3 + - - +
79D ASN* 5.3 1.5 + - - +
81D ILE* 6.1 0.2 - - + -
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PRO* 3.7 16.2 - - - +
191C HIS* 2.5 27.6 + - - +
193C SER* 2.9 3.3 + - - -
195C LEU* 1.3 81.1 - - - +
197C ALA* 1.3 63.9 + - - +
198C SER 3.4 2.0 - - - -
199C ARG* 2.8 32.7 + - - +
24D MET* 3.1 35.2 - - - +
28D GLU* 5.4 3.6 - - - -
31D GLU* 6.0 0.2 - - - -
32D VAL* 4.9 2.9 - - - -
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN* 3.5 15.0 - - - +
191C HIS 3.7 6.3 - - - -
192C PRO* 3.3 29.6 - - + +
193C SER 2.7 11.9 + - - +
194C PRO* 3.5 6.3 + - + +
196C SER* 1.3 71.9 - - - +
198C SER* 1.3 57.1 + - - +
201C PHE* 2.9 34.8 + - + -
202C PHE* 3.1 27.8 + - + -
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Residues in contact with SER 198 (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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194C PRO 4.6 7.1 + - - -
195C LEU 5.4 1.4 + - - -
197C ALA* 1.3 73.2 - - - +
199C ARG* 1.3 63.2 + - - +
200C GLY 3.1 7.4 + - - -
202C PHE* 3.7 19.6 - - - -
73D GLN* 5.3 4.0 + - - -
77D GLY 5.6 1.4 + - - -
11I GLU* 4.1 25.1 + - - +
54I THR 3.6 12.5 - - - +
56I PRO* 3.2 21.2 - - - +
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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