Contacts of the strand formed by residues 222 - 232 (chain A) in PDB entry 1OFU
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 GLY 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 5.7 5.8 - - - -
158A VAL* 5.2 4.5 - - - -
159A ASP 2.8 11.8 + - - -
160A SER* 3.2 5.4 - - - -
161A LEU* 2.8 27.8 + - - -
220A GLU 3.7 1.0 - - - -
221A MET* 1.3 76.8 - - - +
223A MET* 1.3 70.8 + - - -
224A ALA* 4.5 0.3 - - - +
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Residues in contact with MET 223 (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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151A ILE* 5.0 8.3 - - + -
155A ALA* 3.9 20.2 - - + -
161A LEU* 3.6 35.0 - - - +
163A THR* 4.9 7.9 - - - +
221A MET 4.0 1.2 + - - -
222A GLY* 1.3 73.2 - - - -
224A ALA* 1.3 60.2 + - - +
315A GLY 3.1 24.3 + - - -
316A LEU* 3.3 26.8 + - + +
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Residues in contact with ALA 224 (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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160A SER* 4.7 1.6 - - - -
161A LEU 2.9 11.7 + - - +
162A ILE* 3.9 23.8 - - + -
163A THR* 3.0 19.8 + - - -
222A GLY 4.5 2.5 - - - +
223A MET* 1.3 78.5 - - - +
225A MET* 1.3 75.3 + - - +
312A VAL* 4.6 1.3 - - + -
313A ALA 3.1 16.4 - - - +
314A THR* 3.8 19.1 - - + -
316A LEU* 4.1 3.1 - - - -
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Residues in contact with MET 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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162A ILE* 4.3 9.2 - - - -
163A THR* 3.8 24.2 - - + +
165A PRO* 4.7 11.2 - - - -
224A ALA* 1.3 84.3 - - - +
226A MET* 1.3 62.3 + - - +
249A LEU 3.7 21.3 - - - +
250A LEU* 3.7 9.3 - - + +
252A ASP* 4.4 16.2 - - + +
253A VAL* 3.2 35.9 - - + -
312A VAL* 3.5 2.6 - - - +
313A ALA* 2.8 31.0 + - - +
316A LEU* 4.0 10.7 - - + +
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Residues in contact with MET 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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162A ILE* 4.4 16.9 - - + +
163A THR 5.2 1.2 + - - -
164A ILE* 5.3 8.3 - - + -
189A VAL* 4.7 9.4 - - - +
192A GLY 4.6 0.2 - - - -
193A ALA* 3.1 48.0 - - + +
225A MET* 1.3 76.8 - - - +
227A GLY* 1.3 58.7 + - - +
228A THR* 4.1 21.8 - - - -
249A LEU* 3.1 35.6 + - + +
250A LEU* 3.5 7.4 - - - -
310A THR* 3.6 13.2 - - + -
311A VAL 3.0 13.0 - - - +
312A VAL* 3.4 26.5 - - + -
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Residues in contact with GLY 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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226A MET* 1.3 74.9 - - - +
228A THR* 1.3 65.3 + - - +
244A ALA* 3.6 19.0 - - - +
247A ASN* 3.8 12.1 - - - -
249A LEU* 4.8 1.1 - - - -
250A LEU* 3.6 6.7 - - - +
310A THR* 4.1 0.2 - - - +
311A VAL* 2.9 38.3 + - - +
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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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189A VAL* 6.4 0.9 - - + -
192A GLY* 5.5 7.9 - - - +
226A MET* 4.1 14.6 - - - -
227A GLY* 1.3 80.2 - - - +
229A GLY* 1.3 58.2 - - - +
243A ALA* 3.8 3.1 - - - +
244A ALA* 3.6 10.4 - - - -
247A ASN* 3.2 24.5 + - - +
249A LEU* 5.9 2.7 - - + +
309A VAL 3.3 7.6 - - - -
310A THR* 3.8 25.6 - - + +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A THR* 1.3 77.4 - - - +
230A CYS* 1.3 61.8 + - - +
240A ALA 3.7 19.7 - - - -
243A ALA* 4.1 7.4 - - - -
244A ALA* 3.8 4.8 - - - +
308A HIS* 3.4 3.2 + - - +
309A VAL 2.8 32.5 + - - -
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Residues in contact with CYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A GLY* 1.3 74.4 - - - -
231A ALA* 1.3 65.7 + - - +
240A ALA* 3.8 5.7 - - - +
243A ALA* 4.7 4.6 - - - +
306A GLU* 5.7 2.5 - - + -
307A LEU 3.1 10.3 - - - +
308A HIS* 3.4 35.2 - - + +
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Residues in contact with ALA 231 (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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230A CYS* 1.3 78.4 - - - +
232A SER* 1.3 61.1 + - - +
236A ARG* 3.5 30.7 - - - +
239A GLU* 3.7 27.4 - - + +
240A ALA 3.7 2.2 - - - +
306A GLU* 3.4 4.4 - - - -
307A LEU 2.9 30.7 + - - +
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Residues in contact with SER 232 (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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231A ALA* 1.3 75.1 - - - +
233A GLY* 1.3 67.0 + - - +
235A ASN 5.0 0.2 + - - -
236A ARG* 3.7 2.8 - - - +
239A GLU* 3.8 15.2 - - - +
305A ASP* 3.2 32.8 + - - +
306A GLU* 4.6 4.3 - - - -
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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