Contacts of the helix formed by residues 193 - 199 (chain C) in PDB entry 5ITY
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE 3.7 0.4 - - - +
158C ASP* 3.4 30.6 + - - +
159C ARG 4.0 0.9 - - - -
191C PHE 3.6 3.2 + - - -
192C GLU* 1.3 77.6 + - - +
194C ALA* 1.3 68.6 + - - +
195C ARG* 3.2 46.2 + - + +
196C SER* 3.3 27.3 + - - +
197C VAL* 3.3 14.1 + - - +
287C PRO* 5.1 1.0 - - + +
288C LEU* 3.9 21.7 - - + +
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Residues in contact with ALA 194 (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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157C PHE* 3.4 22.7 - - + +
159C ARG 2.9 22.8 + - - +
161C ILE* 3.9 16.6 - - + +
164C ALA* 3.5 26.9 - - + -
192C GLU 3.4 2.0 + - - -
193C LYS* 1.3 70.6 - - - +
195C ARG* 1.3 63.9 + - - +
197C VAL* 3.2 6.4 - - - +
198C LEU* 3.0 26.8 + - - +
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Residues in contact with ARG 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 2.7 37.7 + - + +
153C ALA* 3.5 7.6 - - - +
154C ASP 3.0 23.0 + - - +
157C PHE* 3.2 13.7 + - + +
158C ASP* 2.7 30.3 + - - -
193C LYS* 3.2 38.6 - - + +
194C ALA* 1.3 77.4 - - - +
196C SER* 1.3 65.8 + - - +
198C LEU* 2.9 17.3 + - - +
199C GLU* 2.9 37.7 + - + +
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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
----------------------------------------------------------
192C GLU* 3.4 26.3 + - - -
193C LYS* 3.5 21.1 - - - +
195C ARG* 1.3 76.2 - - - +
197C VAL* 1.3 66.8 + - - +
199C GLU* 2.7 26.0 + - - +
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Residues in contact with VAL 197 (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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161C ILE* 4.3 15.0 - - + -
188C ILE* 4.3 23.3 - - + -
192C GLU* 3.8 24.2 - - + +
193C LYS 3.3 15.5 - - - +
194C ALA* 3.2 7.2 - - - +
196C SER* 1.3 81.4 - - - +
198C LEU* 1.3 67.0 + - + +
199C GLU 3.1 8.0 + - - +
200C ALA* 4.0 7.1 - - - +
225C LEU* 4.1 27.8 - - + -
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Residues in contact with LEU 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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148C VAL* 4.3 5.6 - - + -
149C LEU* 4.5 20.0 - - + +
152C LEU* 3.7 27.7 - - + +
157C PHE* 3.7 36.6 - - + -
161C ILE* 4.7 11.0 - - + -
171C PHE* 5.0 4.5 - - + -
194C ALA 3.0 14.3 + - - +
195C ARG* 2.9 11.2 + - - +
197C VAL* 1.3 76.9 - - + +
199C GLU* 1.3 51.6 + - - +
200C ALA* 2.6 24.7 + - - -
225C LEU* 4.3 21.5 - - + -
226C LEU* 4.5 17.9 - - + -
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Residues in contact with GLU 199 (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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152C LEU* 3.9 14.1 - - + +
195C ARG* 3.1 35.4 + - + +
196C SER* 2.7 36.3 - - - +
197C VAL 3.1 5.3 + - - +
198C LEU* 1.3 70.0 - - - +
200C ALA* 1.3 65.5 + - - +
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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