Contacts of the helix formed by residues 190 - 195 (chain A) in PDB entry 4X8G
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A SER* 3.3 26.0 - - - +
85A GLY* 4.0 14.4 - - - +
86A SER* 3.8 26.2 - - - +
87A THR* 4.3 4.9 - - - +
111A THR* 3.9 9.0 - - + -
112A GLY 4.2 4.0 - - - +
113A VAL* 4.1 12.6 - - + -
189A THR* 1.3 103.3 + - - +
191A LYS* 1.3 65.7 + - - +
192A ASP* 4.5 2.9 - - - +
193A PHE* 3.3 24.4 - - + +
242A GLY* 3.5 4.9 - - - -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY 4.8 3.0 + - - -
190A PRO* 1.3 69.7 - - - +
192A ASP* 1.3 60.6 + - - +
193A PHE 3.1 7.6 + - - -
194A PHE* 4.1 6.1 + - - +
242A GLY* 3.9 24.1 + - - -
243A GLY* 4.3 2.1 - - - +
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 5.0 2.3 - - - -
87A THR* 2.9 36.7 + - - +
190A PRO* 4.5 4.0 - - - +
191A LYS* 1.3 75.2 + - + +
193A PHE* 1.3 62.4 + - - +
194A PHE 3.2 3.1 - - - -
195A THR* 3.2 28.3 - - + +
196A ASN* 4.4 3.5 + - - +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.7 20.0 - - + -
87A THR* 4.4 8.5 - - + +
111A THR* 4.5 12.6 - - + -
113A VAL* 3.6 30.7 - - + -
115A ILE* 5.3 1.6 - - + -
189A THR* 3.5 19.1 - - + -
190A PRO* 3.3 28.2 - - + +
191A LYS 3.1 1.6 - - - -
192A ASP* 1.3 79.8 - - - +
194A PHE* 1.3 90.7 + + - +
195A THR 3.4 0.4 - - - -
196A ASN* 3.1 18.1 - - - +
197A HIS* 3.4 39.2 - + + +
271A LEU* 4.4 14.1 - - + -
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 5.6 0.9 - - + -
187A THR* 5.4 5.6 - - - -
189A THR* 4.4 10.8 - - + -
191A LYS 4.1 7.4 + - - +
192A ASP 3.2 1.2 - - - -
193A PHE* 1.3 114.1 - + - +
195A THR* 1.3 60.7 + - - +
196A ASN 3.2 2.2 - - - -
197A HIS* 3.2 28.4 - - + +
198A THR* 5.4 1.6 - - - -
199A LEU* 4.1 30.3 - - + -
240A VAL* 2.9 53.4 - - + +
241A PRO* 4.0 13.0 - - + -
242A GLY* 4.9 4.7 - - - +
271A LEU* 5.2 2.7 - - + -
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS 5.5 0.2 + - - -
192A ASP* 3.2 26.3 + - + +
194A PHE* 1.3 79.2 - - - +
196A ASN* 1.3 72.9 + - + +
274A THR* 4.9 1.0 + - - -
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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