Contacts of the strand formed by residues 176 - 184 (chain C) in PDB entry 4I7C
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 VAL 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C LEU* 4.0 18.8 - - + +
173C PRO 3.7 16.6 - - - +
174C GLY 3.3 15.7 + - - +
175C ALA* 1.3 75.9 - - - +
177C ASP* 1.3 78.9 + - - +
178C TRP* 3.8 20.6 - - + -
194C GLU* 4.2 0.3 - - - +
195C LYS* 2.9 35.0 + - + +
122D PRO* 3.5 28.5 - - + -
123D TRP 3.2 15.9 - - - +
124D VAL* 4.7 10.5 - - + -
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Residues in contact with ASP 177 (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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131C PRO* 4.1 22.3 - - + +
176C VAL* 1.3 80.7 - - - +
178C TRP* 1.3 64.1 + - - +
192C VAL* 5.2 0.9 - - + +
193C LEU 3.5 3.9 - - - +
194C GLU* 3.4 16.7 - - - +
603C MPD 4.5 12.6 + - + +
122D PRO* 3.5 4.7 - - - +
123D TRP* 2.7 41.6 + - + +
125D ARG* 2.7 56.9 + - - +
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Residues in contact with TRP 178 (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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165C PHE* 3.7 13.2 - - + -
167C ALA* 3.7 13.2 - - + -
168C THR 3.0 29.5 + - - +
169C ASP 3.7 14.1 - - - -
170C ILE* 3.9 18.6 - - + -
172C LEU 5.6 0.4 - - - -
176C VAL* 3.8 20.6 - - + -
177C ASP* 1.3 77.0 - - - +
179C VAL* 1.3 68.2 + - - +
191C LEU 3.9 0.2 - - - +
192C VAL* 3.5 3.5 - - - +
193C LEU* 2.8 61.2 + - + +
195C LYS* 3.9 29.6 - - + -
205C PHE* 4.4 7.4 - + - -
120D VAL* 3.3 35.6 + - + -
121D ARG 5.0 1.3 - - - -
122D PRO* 3.4 23.7 - - + +
123D TRP* 5.4 1.1 - - - -
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Residues in contact with VAL 179 (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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131C PRO* 3.4 35.0 - - + -
154C SER 5.6 0.2 - - - +
155C ILE* 4.2 31.0 - - + +
156C CYS 5.2 0.7 + - - -
165C PHE* 4.5 0.7 - - - -
178C TRP* 1.3 82.4 - - - +
180C MET* 1.3 68.8 + - - +
190C MET* 3.7 35.4 - - + -
191C LEU 3.4 6.1 - - - +
192C VAL* 4.4 3.6 - - + -
603C MPD 3.9 20.5 - - + +
120D VAL* 3.8 13.6 - - - +
123D TRP* 5.3 4.7 + - + -
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Residues in contact with MET 180 (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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155C ILE* 4.0 5.4 - - - -
156C CYS 3.7 11.2 - - - +
158C LEU* 3.9 11.7 - - + +
163C ILE* 3.5 29.8 - - + -
165C PHE* 4.2 17.7 - - + -
179C VAL* 1.3 78.4 - - - +
181C MET* 1.3 83.7 + - - +
190C MET* 3.6 4.3 - - - -
191C LEU* 2.9 42.9 + - + +
118D 23P 3.7 32.8 - - + +
120D VAL* 3.7 28.7 - - + -
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Residues in contact with MET 181 (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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145C MET* 3.5 20.6 - - + -
148C LEU* 4.1 6.7 - - + -
155C ILE* 3.6 20.2 - - + +
156C CYS 3.1 4.6 + - - -
157C THR* 3.3 29.7 - - + +
158C LEU 2.9 24.3 + - - -
180C MET* 1.3 86.0 - - - +
182C GLN* 1.3 60.5 + - - +
188C HIS* 3.7 14.4 - - + +
189C PHE 3.3 13.0 - - - +
190C MET* 3.8 33.4 - - - -
191C LEU* 4.6 0.7 - - - -
212C ILE* 3.2 30.7 - - + -
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Residues in contact with GLN 182 (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 THR* 4.6 0.7 - - - -
158C LEU* 3.5 5.4 - - - +
160C GLY 3.0 27.2 + - - +
161C GLU* 3.3 24.5 + - - +
162C ASP 3.5 2.6 - - - +
163C ILE* 3.6 17.0 - - + +
181C MET* 1.3 74.6 - - - +
183C SER* 1.3 58.6 + - - +
184C CYS* 4.2 1.5 - - - -
188C HIS* 3.6 0.8 - - - -
189C PHE* 2.7 43.5 + - - -
191C LEU* 3.3 22.6 - - + +
277C VAL* 3.1 34.9 + - - +
279C ILE* 3.7 22.6 - - + +
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Residues in contact with SER 183 (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 THR* 4.1 3.3 - - - +
158C LEU 2.9 10.7 + - - -
159C GLN* 3.1 38.9 + - - +
160C GLY 3.0 24.1 + - - -
181C MET 4.2 0.4 - - - -
182C GLN* 1.3 72.3 - - - +
184C CYS* 1.3 64.4 + - - +
186C GLY* 5.7 1.6 + - - -
187C PHE 3.4 11.6 + - - -
188C HIS* 3.7 25.9 + - - -
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Residues in contact with CYS 184 (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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160C GLY* 3.6 23.6 - - - +
161C GLU* 3.8 12.3 - - + +
182C GLN* 4.6 1.1 - - - -
183C SER* 1.3 77.6 + - - +
185C PHE* 1.3 84.9 + - + +
186C GLY 3.1 3.6 - - - +
187C PHE* 3.0 18.5 + - - +
189C PHE* 3.6 25.8 - - - -
279C ILE* 3.8 21.8 - - - -
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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