Contacts of the strand formed by residues 185 - 190 (chain C) in PDB entry 4ERQ
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 LEU 185 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C PHE* 3.3 9.9 - - - -
180C ASN* 2.9 49.4 + - - +
183C GLY 3.2 0.2 - - - -
184C SER* 1.3 94.2 - - - +
186C ILE* 1.3 63.8 + - - +
197C ILE* 4.1 8.1 - - + -
198C TRP 3.3 7.4 - - - +
199C ASP* 4.5 2.2 - - - +
200C THR* 3.7 0.7 - - - -
206C LEU* 3.6 31.0 - - + -
222C PHE* 4.0 15.7 - - + -
226C GLY 5.9 1.1 - - - +
243C TYR* 3.8 33.4 - - + +
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Residues in contact with ILE 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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145C VAL* 4.0 20.0 - - + -
153C VAL* 4.8 4.7 - - + -
155C ILE* 3.6 36.1 - - + -
167C LEU* 5.1 2.0 - - + -
177C VAL* 4.8 3.1 - - + -
178C HIS 3.3 10.3 - - - +
179C PHE* 3.4 39.0 - - + -
185C LEU* 1.3 73.0 - - - +
187C VAL* 1.3 73.4 + - - +
188C SER* 4.6 0.7 - - - +
197C ILE* 3.2 4.6 - - - +
198C TRP* 2.7 57.5 + - + +
200C THR* 3.7 9.2 - - - +
222C PHE* 4.1 3.1 - - - -
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Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ALA 4.0 0.2 - - - +
177C VAL* 3.3 4.7 - - - -
178C HIS* 2.9 44.2 + - + +
186C ILE* 1.3 75.5 - - - +
188C SER* 1.3 66.2 + - - +
195C CYS* 4.7 2.2 - - + -
196C ARG 3.2 10.8 - - - +
197C ILE* 4.0 15.5 - - + -
220C VAL* 3.8 34.5 - - + +
221C LYS* 4.2 9.6 - - - -
222C PHE* 3.6 34.6 - - + +
229C ILE* 4.0 11.4 - - + -
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Residues in contact with SER 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C VAL* 4.0 20.4 - - - +
170C HIS* 2.8 27.5 + - - -
174C VAL* 4.4 0.9 - - - -
176C ALA 3.3 10.1 - - - -
177C VAL* 4.2 2.9 - - - -
186C ILE* 5.1 0.7 - - - -
187C VAL* 1.3 76.8 - - - +
189C SER* 1.3 60.5 + - - +
195C CYS* 3.3 6.2 - - - +
196C ARG* 2.7 32.3 + - - +
198C TRP* 2.9 25.7 + - - -
220C VAL* 3.8 2.9 - - - -
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 4.1 1.8 - - - -
174C VAL* 3.4 7.8 - - - +
175C SER* 2.8 39.9 + - - -
176C ALA* 3.1 24.9 + - - +
188C SER* 1.3 74.6 - - - +
190C SER* 1.3 65.4 + - - +
194C LEU 3.5 6.5 - - - -
195C CYS* 4.5 1.1 - - - -
217C VAL* 3.5 26.7 - - - -
219C PHE 3.8 3.3 - - - -
220C VAL* 3.6 13.6 - - - +
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Residues in contact with SER 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 3.2 31.0 - - - -
172C ASP 3.0 13.3 + - - -
173C PRO 2.8 21.5 + - - -
175C SER* 3.7 2.2 + - - -
189C SER* 1.3 77.4 - - - +
191C TYR* 1.3 57.8 + - - +
192C ASP* 2.9 19.0 + - - +
193C GLY* 3.0 17.7 + - - -
194C LEU 3.2 6.1 + - - -
217C VAL* 3.1 22.8 + - - +
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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