Contacts of the strand formed by residues 185 - 191 (chain C) in PDB entry 4F2N
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 ARG 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.6 60.1 - - + +
160C CYS* 4.2 1.8 - - - -
161C VAL* 2.8 42.2 + - + +
163C PRO* 3.6 29.2 - - + +
183C GLY 4.5 5.4 + - - +
184C LEU* 1.3 76.0 - - - +
186C PRO* 1.3 68.7 - - - +
187C ILE* 3.6 2.3 + - - +
227C ARG 4.7 0.4 + - - -
228C ALA* 2.9 46.3 + - + -
230C LYS 4.4 9.9 + - - -
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Residues in contact with PRO 186 (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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23C TYR* 5.2 0.7 + - - -
25C THR* 3.4 30.0 + - + +
106C PHE* 4.3 10.8 - - + -
110C PHE* 3.5 13.0 - - + -
158C TRP* 3.6 37.9 - - + -
159C LEU 3.7 5.8 - - - +
160C CYS* 4.0 6.9 - - - -
179C PRO* 4.5 9.6 - - + -
180C LEU* 5.1 5.4 - - + +
184C LEU 3.5 10.7 - - - +
185C ARG* 1.3 84.0 - - - +
187C ILE* 1.3 62.8 + - - +
224C MET* 3.9 13.9 - - - +
228C ALA* 5.6 0.2 - - - +
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Residues in contact with ILE 187 (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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110C PHE* 3.5 12.6 - - - -
114C CYS* 4.2 2.1 - - - -
126C LEU* 4.2 4.9 - - + -
159C LEU* 2.8 38.6 + - + +
160C CYS 4.7 0.2 - - - +
161C VAL* 4.0 9.6 - - + -
168C LEU* 3.6 29.2 - - + -
185C ARG 3.9 8.7 - - - +
186C PRO* 1.3 78.0 - - - +
188C PHE* 1.3 59.8 + - - +
220C PHE* 4.7 0.2 - - - -
221C VAL* 3.3 38.8 - - + +
224C MET* 3.7 18.4 - - + +
225C TYR* 3.7 35.7 - - + +
228C ALA* 4.5 2.0 - - + -
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Residues in contact with PHE 188 (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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110C PHE* 3.6 8.1 - - - -
114C CYS* 3.7 24.0 - - + -
115C LEU* 4.9 3.1 - - + -
140C PHE* 5.2 2.2 - + - -
144C PHE* 3.5 37.5 - + - -
158C TRP* 3.4 6.9 - - - -
159C LEU* 2.9 39.7 + - + +
187C ILE* 1.3 79.2 - - - +
189C THR* 1.3 85.9 + - - +
212C LEU* 4.3 13.7 - - + -
213C TRP* 3.8 19.1 - + - -
216C VAL* 3.6 37.0 - - + -
218C TRP* 5.0 3.4 - + + -
221C VAL* 3.9 22.4 - - + -
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Residues in contact with THR 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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107C ASN 4.3 1.3 - - - +
110C PHE* 3.8 18.2 - - + -
111C PHE* 3.4 39.2 - - + +
114C CYS* 3.9 2.7 - - - +
156C TRP* 3.6 19.3 - - + +
157C THR 3.2 12.3 + - - -
158C TRP* 3.3 34.1 - - + -
188C PHE* 1.3 99.1 - - - +
190C ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 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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111C PHE* 3.9 5.2 - - - -
144C PHE* 3.6 24.0 - - + -
156C TRP* 3.5 4.9 - - - -
157C THR* 2.8 33.1 + - - +
189C THR* 1.3 74.5 - - - +
191C ASP* 1.3 65.0 + - - +
192C VAL* 3.4 4.2 + - + +
209C LEU* 3.9 13.2 - - + -
212C LEU* 3.5 26.9 - - + -
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Residues in contact with ASP 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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58C HIS* 2.7 32.4 + - - -
108C HIS* 3.4 8.7 + - - -
111C PHE* 3.6 25.4 - - + -
155C GLY 3.7 0.7 - - - +
156C TRP* 3.4 30.9 - - + -
190C ALA* 1.3 69.8 - - - +
192C VAL* 1.3 59.5 + - - +
193C TRP* 3.2 31.3 + - - +
195C HIS* 3.6 2.6 + - - -
196C ALA* 3.6 14.3 - - + +
208C TYR* 2.8 32.1 + - - -
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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