Contacts of the strand formed by residues 188 - 198 (chain C) in PDB entry 5MWF
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 ALA 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU* 4.3 17.5 - - + -
38C ARG 3.1 18.2 - - - +
39C ASN* 4.4 3.8 - - + -
148C ALA* 5.8 0.4 - - + -
163C ILE* 4.6 4.0 - - + -
164C GLU* 3.2 24.6 + - + +
183C PHE 4.2 0.2 - - - +
185C GLY* 2.9 27.4 + - - -
187C VAL* 1.3 84.2 - - + +
189C HIS* 1.3 66.5 + - - +
190C LEU* 4.5 5.7 - - + +
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Residues in contact with HIS 189 (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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291B TRP* 5.4 1.4 - - + -
37C LEU* 3.3 5.9 - - - +
38C ARG* 3.0 76.0 + - + +
40C VAL* 6.3 1.6 - - + -
183C PHE 3.2 7.4 - - - +
184C SER* 2.8 40.1 + - - -
185C GLY 4.2 9.3 + - - -
187C VAL 4.7 4.0 - - - -
188C ALA* 1.3 82.8 - - - +
190C LEU* 1.3 64.8 + - - +
191C GLU* 6.5 0.2 - - + -
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Residues in contact with LEU 190 (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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34C LEU* 4.5 12.3 - - + -
36C ALA 3.5 6.5 - - - +
37C LEU* 3.6 26.9 - - + -
71C VAL* 5.6 2.9 - - + -
146C VAL* 4.5 22.2 - - + +
147C GLU 5.9 1.6 - - - -
148C ALA* 5.2 5.8 - - + -
164C GLU* 4.6 9.9 - - + -
166C VAL* 4.5 17.0 - - + -
181C LEU 3.9 0.9 - - - +
182C HIS* 3.7 3.6 - - - -
183C PHE* 3.0 51.0 + - + +
188C ALA* 4.5 9.2 - - + +
189C HIS* 1.3 85.4 - - - +
191C GLU* 1.3 66.2 + - - +
192C LEU* 4.2 12.3 - - + -
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Residues in contact with GLU 191 (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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266B TYR* 3.6 46.5 + - + +
291B TRP* 5.5 1.1 - - + -
34C LEU* 3.4 2.6 - - - +
35C SER* 2.9 38.5 + - - +
36C ALA* 3.1 20.8 + - + -
180C SER* 5.6 0.9 - - - -
181C LEU 3.7 3.7 + - - +
182C HIS* 2.7 44.2 + - - +
189C HIS* 6.0 0.4 - - + -
190C LEU* 1.3 77.8 - - - +
192C LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 192 (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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32C LEU* 4.1 15.7 - - + -
33C GLN 3.2 15.9 - - - +
34C LEU* 4.0 12.1 - - + -
35C SER* 4.4 3.1 - - - -
144C LEU* 4.7 1.6 - - + -
146C VAL* 4.4 25.6 - - + -
180C SER* 3.6 1.9 - - - -
181C LEU* 2.9 47.7 + - + +
183C PHE* 3.9 26.5 - - + -
190C LEU* 4.6 11.7 - - + -
191C GLU* 1.3 75.9 + - - +
193C GLN* 1.3 70.8 + - - +
194C ILE* 3.9 23.8 - - + -
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Residues in contact with GLN 193 (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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265B SER* 5.7 6.3 - - - +
266B TYR* 5.6 8.3 - - - +
32C LEU* 3.3 4.5 - - - +
33C GLN* 2.8 46.0 + - + +
35C SER* 5.8 6.7 + - - +
178C TRP* 3.6 36.3 - - + +
179C LYS 3.2 11.7 - - - +
180C SER* 4.0 21.1 + - - +
192C LEU* 1.3 79.7 - - - +
194C ILE* 1.3 65.8 + - - +
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Residues in contact with ILE 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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30C PHE* 3.9 13.9 - - + -
31C GLU 3.4 8.1 - - - +
32C LEU* 3.8 27.6 - - + -
142C PHE* 3.6 33.4 - - + -
144C LEU* 4.2 5.2 - - + -
168C HIS* 5.0 1.8 - - + +
172C ILE* 3.8 16.3 - - + +
177C ARG 3.3 1.2 - - - +
178C TRP* 3.3 5.2 - - - -
179C LYS* 2.8 41.6 + - + +
181C LEU* 4.0 17.7 - - + -
192C LEU* 3.9 10.3 - - + -
193C GLN* 1.3 80.7 - - - +
195C ARG* 1.3 63.7 + - - +
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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
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29C TYR* 4.6 4.0 + - - -
30C PHE* 3.9 2.5 - - - -
31C GLU* 2.8 62.2 + - + +
172C ILE* 3.7 10.5 - - - -
177C ARG* 3.4 31.0 - - - +
178C TRP* 3.4 48.5 - - + +
194C ILE* 1.3 78.0 - - - +
196C VAL* 1.3 71.1 + - - +
197C ARG* 3.7 31.0 - - + +
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Residues in contact with VAL 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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29C TYR 3.8 3.6 - - - +
30C PHE* 3.6 23.1 - - + -
134C PHE* 3.9 29.8 - - + -
138C TRP* 3.8 19.3 - - + +
172C ILE* 3.7 26.9 - - + +
173C ASN 4.8 1.5 + - - -
174C PRO* 3.2 42.1 - - + +
177C ARG* 6.0 1.1 - - - +
195C ARG* 1.3 83.2 - - - +
197C ARG* 1.3 72.0 + - - +
207C CYS* 4.8 3.4 - - - -
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Residues in contact with ARG 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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28C GLY* 3.2 2.8 - - - -
29C TYR* 2.9 71.9 + - + +
31C GLU* 4.4 0.4 - - - +
174C PRO* 4.8 9.2 + - - +
195C ARG* 3.7 38.8 - - + +
196C VAL* 1.3 79.9 + - - +
198C CYS* 1.3 72.3 + - - +
207C CYS* 4.2 5.8 - - - -
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Residues in contact with CYS 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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27C MET 3.7 2.5 - - - +
28C GLY* 4.2 0.4 - - - -
29C TYR* 4.4 4.8 - - - -
174C PRO* 4.3 11.3 - - - +
197C ARG* 1.3 95.0 + - - +
199C ASP* 1.3 64.4 + - - +
202C TYR* 3.8 22.9 - - + +
203C TYR* 4.5 1.6 - - - -
204C SER 3.8 12.1 - - - -
207C CYS* 2.0 56.3 - - + -
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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