Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 6C90
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 CYS 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.9 39.7 - - + -
179A LEU* 4.5 3.8 - - + -
185A VAL* 3.4 18.8 - - + -
187A PHE* 4.9 5.6 - - - -
202A MET* 5.0 2.9 - - - -
208A ASP 3.3 11.3 + - - +
209A VAL* 3.2 21.4 - - + +
210A GLY 2.8 30.8 + - - -
222A ALA* 3.6 1.7 - - - +
223A SER* 1.3 76.7 - - - +
225A LEU* 1.3 62.7 + - - +
226A VAL* 4.7 6.7 - - - -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 4.0 11.7 - - - +
185A VAL 3.0 10.9 + - - +
186A ILE* 3.3 10.0 - - + +
187A PHE 3.0 24.5 + - - +
210A GLY* 3.8 11.4 - - - -
212A MET* 4.0 19.3 - - - -
219A ASN 3.9 14.6 - - - +
220A PRO* 3.7 28.0 - - + +
222A ALA* 3.9 14.1 - - + +
224A CYS* 1.3 74.2 - - - +
226A VAL* 1.3 64.0 - - - +
227A MET* 3.6 18.4 - - + -
242A VAL* 3.7 30.5 - - + -
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 3.2 26.9 - - + +
189A SER* 5.0 0.7 - - - +
195A SER* 3.7 33.4 - - - +
198A LYS* 4.3 11.0 - - + +
199A TYR* 4.1 15.5 - - - +
202A MET* 4.6 8.1 - - + -
209A VAL* 3.9 17.9 - - + -
210A GLY 2.9 15.2 + - - +
211A LEU* 3.2 11.7 - - + +
212A MET* 2.9 24.9 + - - +
224A CYS* 4.7 2.7 - - - -
225A LEU* 1.3 70.8 - - - +
227A MET* 1.3 66.1 + - - +
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Residues in contact with MET 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 3.7 37.9 - - + -
187A PHE 3.0 6.5 + - - +
188A THR* 3.2 27.7 - - + -
189A SER 3.2 6.1 + - - -
195A SER* 3.6 8.7 + - - -
211A LEU* 4.9 1.6 - - - -
212A MET* 3.1 25.1 - - + +
225A LEU* 3.6 33.9 - - + -
226A VAL* 1.3 75.9 - - - +
228A THR* 1.3 68.1 + - - +
231A ILE* 4.3 2.0 - - + -
232A LEU* 3.9 18.6 - - - -
235A MET* 3.3 35.7 - - + -
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A THR* 4.8 0.7 - - - -
189A SER 3.6 5.6 - - - +
191A ILE* 4.0 4.0 - - - +
192A LYS* 3.7 38.4 - - + +
195A SER* 3.6 15.5 - - - +
212A MET 3.4 2.2 + - - -
213A THR* 4.0 10.7 - - + -
214A GLY 4.5 1.7 + - - -
227A MET* 1.3 82.8 - - - +
229A THR* 1.3 66.2 + - - +
230A GLU* 3.4 20.3 + - - +
231A ILE* 3.2 27.5 + - - +
232A LEU* 3.2 16.8 + - - +
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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