Contacts of the helix formed by residues 193 - 199 (chain A) in PDB entry 5ITX
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 LYS 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE 4.1 2.5 - - - +
158A ASP* 3.9 26.8 + - - +
159A ARG 4.2 0.2 - - - -
161A ILE* 4.4 0.9 - - - -
191A PHE 3.7 0.8 + - - -
192A GLU* 1.3 84.6 + - - +
194A ALA* 1.3 67.8 + - - +
195A ARG* 3.8 34.5 - - + +
196A SER* 3.0 32.3 + - - +
197A VAL* 3.2 11.8 + - - +
287A PRO* 4.7 0.8 - - + +
288A LEU* 3.9 22.2 - - + +
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Residues in contact with ALA 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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157A PHE* 3.4 16.6 - - + +
159A ARG 3.1 23.5 + - - +
161A ILE* 3.9 28.0 - - + -
164A ALA* 3.9 17.7 - - + -
192A GLU 3.8 1.6 + - - -
193A LYS* 1.3 72.1 - - - +
195A ARG* 1.3 65.2 + - - +
197A VAL* 3.2 11.8 + - - +
198A LEU* 3.2 19.3 + - - +
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Residues in contact with ARG 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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152A LEU* 2.6 38.5 + - + +
153A ALA* 3.4 13.0 + - - +
154A ASP 2.9 20.2 + - - -
157A PHE* 2.9 22.5 + - + +
158A ASP* 2.6 29.9 + - - +
193A LYS* 3.4 22.1 - - - +
194A ALA* 1.3 74.7 - - - +
196A SER* 1.3 57.5 + - - +
198A LEU* 4.5 4.3 - - - -
199A GLU* 3.0 57.5 + - + +
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Residues in contact with SER 196 (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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192A GLU* 3.8 13.4 + - - -
193A LYS* 3.0 30.6 + - - +
195A ARG* 1.3 81.5 - - - +
197A VAL* 1.3 53.6 + - - +
199A GLU* 2.5 31.8 - - - +
200A ALA* 3.7 6.4 - - - +
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Residues in contact with VAL 197 (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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161A ILE* 4.6 8.3 - - + -
188A ILE* 3.8 32.8 - - + -
192A GLU* 3.5 31.0 - - + -
193A LYS 3.2 4.4 + - - +
194A ALA 3.2 8.1 + - - +
196A SER* 1.3 76.3 - - - +
198A LEU* 1.3 57.5 + - + +
199A GLU 3.4 4.3 - - - +
200A ALA* 4.3 4.3 - - - +
201A LEU* 3.6 19.3 + - + +
225A LEU* 3.7 33.0 - - + -
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Residues in contact with LEU 198 (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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148A VAL* 4.0 6.1 - - + -
149A LEU* 4.1 4.5 - - + +
152A LEU* 3.6 23.6 - - + -
157A PHE* 3.6 38.4 - - + -
161A ILE* 4.6 12.1 - - + -
171A PHE* 4.7 3.6 - - + -
194A ALA 3.2 15.9 + - - +
195A ARG 3.9 2.0 - - - +
196A SER 3.1 0.4 - - - -
197A VAL* 1.3 83.1 - - - +
199A GLU* 1.3 61.3 - - - +
201A LEU* 3.0 31.3 - - + +
202A GLN 3.3 7.4 - - - +
203A GLN 4.1 0.2 - - - +
225A LEU* 4.4 15.7 - - + -
226A LEU* 3.9 32.8 - - + -
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Residues in contact with GLU 199 (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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152A LEU* 3.7 7.2 - - + +
195A ARG* 3.0 45.6 + - + +
196A SER* 2.5 28.3 - - - +
198A LEU* 1.3 76.0 + - - +
200A ALA* 1.3 69.4 + - - +
203A GLN 3.4 25.6 - - - +
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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