Contacts of the strand formed by residues 191 - 198 (chain C) in PDB entry 3WHD
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 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C TRP 5.4 3.6 + - - -
170C HIS* 3.3 18.5 - - + +
171C LYS* 6.1 3.0 - - - +
187C TYR* 3.5 11.2 - - - -
188C ASN 3.0 33.4 + - - +
189C GLN* 3.2 7.8 - - + +
190C ASP* 1.3 80.8 - - - +
192C TRP* 1.3 70.2 + - - +
193C ALA* 4.3 9.8 - - - +
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Residues in contact with TRP 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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128C GLN* 3.8 13.5 + - - +
132C ILE* 3.5 57.7 + - + +
135C LEU* 3.5 37.4 + - + -
136C ASP 3.5 16.8 - - - -
137C ARG* 3.7 33.2 - - + +
139C LEU 3.7 8.1 - - - -
141C TYR* 4.2 1.3 - + - -
185C LEU* 3.7 18.6 - - + -
186C VAL* 3.3 33.9 - - - -
187C TYR* 3.4 40.6 - + + -
191C LYS* 1.3 80.5 - - - +
193C ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 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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128C GLN* 4.6 3.1 - - - +
168C PHE* 3.3 14.6 - - + +
169C TRP 4.0 2.0 - - - +
170C HIS* 3.4 36.3 + - + +
185C LEU* 3.6 8.3 - - - +
186C VAL 3.0 32.3 + - - +
191C LYS* 4.3 10.8 - - - +
192C TRP* 1.3 76.5 - - - +
194C TRP* 1.3 68.6 + - - +
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Residues in contact with TRP 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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122C ILE* 4.0 20.7 - - + +
128C GLN* 2.9 26.0 + - - -
143C LEU* 3.6 17.8 - - + +
145C LEU* 4.1 16.4 - - + -
156C TRP* 4.0 22.4 - + - -
162C PHE* 4.9 1.3 - + - -
166C ARG 3.9 6.7 - - - -
167C VAL* 3.8 31.6 - - + -
168C PHE* 2.7 45.7 + + - +
169C TRP* 3.6 37.9 - + + -
170C HIS* 3.0 25.2 + - - -
173C GLU* 3.7 3.6 - - - +
183C VAL* 4.0 13.0 - - + -
184C VAL 3.3 3.4 - - - -
185C LEU* 3.8 9.9 - - + -
193C ALA* 1.3 77.0 - - - +
195C ASN* 1.3 61.1 + - - +
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Residues in contact with ASN 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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140C SER* 5.4 1.0 + - - -
170C HIS* 4.7 1.3 - - + -
173C GLU* 2.9 16.1 - - + +
183C VAL* 3.4 3.7 - - - -
184C VAL* 2.9 41.7 + - + +
186C VAL* 3.6 26.0 - - + +
194C TRP* 1.3 75.6 - - - +
196C ASP* 1.3 62.6 + - - +
197C VAL* 3.8 19.2 + - - +
501C CA 2.4 30.9 - - - -
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Residues in contact with ASP 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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154C TRP* 3.7 24.7 - - + -
169C TRP* 3.9 10.9 - - + -
173C GLU* 2.9 9.9 + - - +
174C PRO* 3.3 11.3 - - - +
175C ASP 2.9 13.5 + - - -
176C ASN* 2.7 33.4 + - + +
181C ASN* 4.7 2.8 + - + -
182C CYS 3.1 11.0 - - - +
183C VAL* 4.2 1.1 - - - -
195C ASN* 1.3 73.8 + - - +
197C VAL* 1.3 63.9 + - - +
501C CA 2.3 57.7 - - - -
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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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140C SER* 6.1 0.2 - - - +
142C PHE* 3.7 27.4 - - + -
176C ASN* 3.6 7.2 + - - +
180C GLU 3.7 0.9 - - - +
181C ASN 3.7 0.7 - - - -
182C CYS 2.7 32.7 + - - +
184C VAL* 4.4 13.5 - - + -
195C ASN* 3.8 22.4 - - - +
196C ASP* 1.3 79.3 - - - +
198C PRO* 1.3 86.9 - - + +
201C PHE* 4.3 15.0 - - + -
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Residues in contact with PRO 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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142C PHE* 4.3 0.7 - - - -
176C ASN* 3.6 13.7 - - - +
178C GLN* 3.4 33.4 - - + +
179C GLY* 4.9 0.7 - - - -
180C GLU 3.4 8.7 - - - +
197C VAL* 1.3 97.8 - - + +
199C CYS* 1.3 65.4 + - - +
200C ASN* 3.5 17.9 - - - +
201C PHE* 3.1 50.6 + - + +
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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