Contacts of the strand formed by residues 193 - 197 (chain H) in PDB entry 5IC4
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 PHE 193 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G THR* 3.6 19.5 - - - -
143G PHE* 3.2 30.1 - - + -
144G ARG* 3.8 5.4 - - + -
145G GLY 4.7 0.2 - - - -
156G LYS* 3.5 23.6 - - + -
158G PHE* 3.7 32.3 - + - -
189H VAL 3.7 20.0 - - - -
190H GLU* 3.4 20.2 + - - +
191H ALA 3.2 20.0 - - - -
192H ASP* 1.3 79.4 - - - +
194H LEU* 1.3 57.9 + - - +
195H TYR* 3.3 37.4 - + + +
266H VAL 4.2 0.3 - - - +
268H MET* 2.8 35.9 + - + -
269H LEU* 3.5 2.3 + - - -
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Residues in contact with LEU 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G LYS 2.9 8.4 + - - +
157G LEU* 3.5 25.3 - - + -
158G PHE* 2.6 36.2 + - - +
159G ILE* 5.9 0.4 - - + -
193H PHE* 1.3 74.9 - - - +
195H TYR* 1.3 59.9 + - - +
196H ALA* 4.0 15.3 - - + +
232H PHE* 3.6 28.9 - - + -
233H MET* 4.3 5.2 - - - -
236H LEU* 3.9 10.3 - - + -
265H ILE* 4.2 13.5 - - + -
266H VAL 3.3 19.1 - - - +
267H SER* 3.6 22.9 - - - +
269H LEU* 3.9 14.6 - - + +
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Residues in contact with TYR 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G LYS* 5.0 5.6 + - - -
140G THR* 3.6 32.2 + - + -
158G PHE* 3.4 21.1 - + + +
160G ILE* 5.0 4.9 - - + -
190H GLU* 4.1 12.3 + - - -
193H PHE* 3.3 39.5 - + + +
194H LEU* 1.3 74.5 - - - +
196H ALA* 1.3 61.2 + - - +
197H TYR* 3.4 37.9 + + + -
264H CYS 3.5 1.0 - - - +
266H VAL* 2.8 57.4 + - + +
268H MET* 3.6 25.7 - - + +
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Residues in contact with ALA 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G PHE 2.8 13.4 + - - +
159G ILE* 3.6 15.7 - - + -
160G ILE* 2.9 25.6 + - - +
194H LEU* 3.9 16.2 - - + +
195H TYR* 1.3 69.6 - - - +
197H TYR* 1.3 64.3 + - - +
215H PHE* 3.7 19.6 - - + -
232H PHE* 5.6 0.4 - - + -
236H LEU* 4.4 16.8 - - + -
264H CYS 4.1 2.2 - - - -
265H ILE* 5.0 4.9 - - + +
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Residues in contact with TYR 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLY* 5.9 2.3 - - - -
136G LEU* 4.2 17.4 - - + +
160G ILE* 3.6 32.3 - - + -
164G ARG* 3.3 55.4 + - + +
195H TYR* 3.5 39.5 - - + +
196H ALA* 1.3 73.6 - - - +
198H SER* 1.3 61.0 + - - +
199H THR 3.6 7.6 - - - +
215H PHE* 3.8 4.5 - - - -
263H PRO* 3.5 6.4 - - - +
264H CYS 3.0 40.9 + - - +
266H VAL* 3.8 17.5 - - + -
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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
------------------------------------------------------------
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