Contacts of the strand formed by residues 193 - 202 (chain C) in PDB entry 5I75
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 TYR 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C LYS* 6.0 3.9 - - - -
125C GLU* 3.8 18.4 + - - +
158C ASN 3.4 1.4 + - - -
159C PHE* 2.8 50.5 + - + +
160C TYR* 3.4 36.5 + + - -
161C PRO* 4.2 1.1 - - + -
162C LYS* 3.9 41.5 - - + -
183C TRP* 5.9 1.8 - - + -
184C THR* 3.6 22.2 - - - +
185C ASP* 4.7 2.7 - - - -
186C GLN* 3.2 47.1 + - + +
192C THR* 1.3 71.0 - - - +
194C SER* 1.3 68.8 + - - +
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Residues in contact with SER 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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189B HIS* 3.4 28.6 + - - -
191B PHE* 4.1 9.4 - - - -
156C LEU 3.3 12.1 - - - -
157C ASN* 3.8 6.4 - - - -
158C ASN 3.4 12.8 + - - -
159C PHE* 3.6 3.4 - - - -
183C TRP* 3.8 1.5 - - - +
184C THR* 2.8 42.4 + - - +
192C THR 4.1 3.3 + - - -
193C TYR* 1.3 81.4 + - - +
195C MET* 1.3 61.5 + - - +
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Residues in contact with MET 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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191B PHE* 3.3 11.1 - - - -
156C LEU* 2.9 51.8 + - + +
159C PHE* 3.7 6.5 - - + -
164C ILE* 3.6 19.7 - - - -
166C VAL* 3.7 22.2 - - + -
181C ASN* 3.6 44.0 - - + +
182C SER 3.0 13.0 - - - +
183C TRP* 3.1 38.4 - - + +
194C SER* 1.3 74.5 - - - +
196C SER* 1.3 64.3 + - - +
197C SER 4.8 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
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191B PHE* 3.5 28.7 - - - +
203B SER* 4.0 5.6 + - - -
154C CYS 3.8 4.3 - - - -
155C PHE* 3.7 19.7 - - - -
180C LEU 3.0 5.9 - - - +
181C ASN* 4.4 0.9 - - - -
182C SER* 2.9 43.5 + - - -
195C MET* 1.3 78.4 - - - +
197C SER* 1.3 60.5 + - - +
198C THR* 3.9 6.7 + - - -
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Residues in contact with SER 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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153C VAL* 3.9 1.4 - - - +
154C CYS* 2.9 41.7 + - - +
156C LEU* 4.3 4.6 - - - +
166C VAL* 3.5 17.0 - - - +
168C TRP* 2.3 40.9 + - - -
179C VAL* 3.4 3.6 - - - +
180C LEU 3.3 4.7 - - - -
181C ASN* 3.2 20.7 + - - -
195C MET 4.3 0.6 - - - -
196C SER* 1.3 71.4 - - - +
198C THR* 1.3 58.9 + - - +
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Residues in contact with THR 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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166B LEU* 5.6 10.2 - - + +
201B THR* 6.1 4.5 - - + -
203B SER* 5.1 5.7 + - - -
151C SER* 4.6 9.9 - - - -
152C VAL 4.1 3.4 - - - +
153C VAL* 4.8 15.0 - - + +
168C TRP* 4.2 1.6 - - - -
178C GLY 2.9 13.5 - - - +
179C VAL* 3.2 3.0 - - - -
180C LEU* 2.9 38.9 + - + +
196C SER* 4.5 9.5 + - - -
197C SER* 1.3 74.8 + - - +
199C LEU* 1.3 63.0 + - - +
200C THR* 3.5 21.3 - - - +
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Residues in contact with LEU 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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150C ALA 4.2 0.2 - - - +
151C SER* 3.2 3.3 - - - -
152C VAL* 2.9 49.6 + - + +
168C TRP* 3.6 35.8 - - + -
170C ILE* 4.1 24.0 - - + -
175C ARG* 3.9 9.9 - - + -
177C ASN 3.6 24.2 - - - +
178C GLY* 3.3 7.9 - - - +
179C VAL* 3.8 13.5 - - + -
198C THR* 1.3 71.4 - - - +
200C THR* 1.3 60.5 + - - +
201C LEU* 3.7 23.0 + - + +
212C TYR* 4.8 6.1 - - + -
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Residues in contact with THR 200 (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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168B LYS* 6.1 6.3 - - + -
196B GLN* 5.8 2.1 + - - -
144C GLN* 5.6 0.9 - - - +
151C SER* 3.3 21.2 + - - +
178C GLY* 3.2 19.5 + - - +
180C LEU* 5.9 2.4 - - - +
198C THR* 3.5 18.0 - - - +
199C LEU* 1.3 69.9 - - - +
201C LEU* 1.3 76.0 + - - +
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Residues in contact with LEU 201 (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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149C GLY* 4.0 1.6 - - - -
150C ALA 2.7 40.8 + - - +
152C VAL* 6.0 2.2 - - + -
170C ILE* 4.1 23.1 - - + -
175C ARG* 4.5 18.4 - - - +
177C ASN 4.9 2.0 - - - +
178C GLY* 5.7 0.7 - - - -
199C LEU* 3.7 27.1 + - + +
200C THR* 1.3 88.7 - - - +
202C THR* 1.3 67.4 + - - +
205C GLU* 4.0 29.2 - - + +
206C TYR* 5.4 4.3 - - + +
209C HIS* 6.3 0.9 - - + -
212C TYR* 4.6 17.0 - - + +
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Residues in contact with THR 202 (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 GLY 4.9 2.9 - - - -
149C GLY* 4.7 3.1 - - - -
150C ALA 4.3 1.6 - - - +
201C LEU* 1.3 79.5 - - - +
203C LYS* 1.3 60.8 + - - +
204C ASP* 4.0 7.8 + - - +
205C GLU* 3.4 27.8 + - - +
206C TYR* 3.0 29.0 + - - +
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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