Contacts of the strand formed by residues 227 - 235 (chain H) in PDB entry 1II4
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 227 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H LYS* 5.5 0.2 - - - -
194H ASN* 3.8 11.9 - - - -
225H ASP 3.4 1.2 + - - -
226H LYS* 1.3 84.8 - - - +
228H ASN* 1.3 64.9 + - - -
229H TYR* 3.4 11.3 - - - -
245H HIS* 3.6 2.5 - - - -
246H LEU 2.8 27.9 + - - -
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Residues in contact with ASN 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LEU 3.4 0.3 - - - +
193H LYS* 3.2 5.7 - - - +
194H ASN* 2.6 52.6 + - - +
227H GLY* 1.3 74.8 - - - -
229H TYR* 1.3 62.6 + - - +
230H THR* 4.1 2.4 + - - +
243H THR* 3.8 21.6 - - + +
244H TYR 3.4 2.0 - - - -
245H HIS* 3.9 19.2 - - - +
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Residues in contact with TYR 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H PHE* 3.7 32.3 - + + -
191H TRP* 4.5 8.1 - - + -
192H LEU 3.1 10.8 - - - +
193H LYS* 3.1 33.2 + - + +
198H PHE* 3.7 16.8 - + - -
216H LEU* 4.1 12.1 - - + -
218H MET* 3.6 32.2 - - + -
225H ASP* 2.6 34.3 + - - -
227H GLY* 3.4 20.6 - - - -
228H ASN* 1.3 75.5 - - - +
230H THR* 1.3 60.5 + - - +
231H CYS 4.3 0.2 + - - -
242H HIS 3.9 0.7 - - - +
243H THR* 3.4 0.5 - - - -
244H TYR* 2.7 45.6 + - - +
246H LEU* 3.7 11.0 - - + -
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Residues in contact with THR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H ARG 3.6 0.3 - - - +
191H TRP* 3.2 6.9 - - - -
192H LEU* 2.6 57.7 + - + +
195H GLY* 5.2 5.0 + - - -
228H ASN* 4.1 3.0 + - - +
229H TYR* 1.3 72.2 - - - +
231H CYS* 1.3 70.5 + - - +
232H VAL* 3.9 10.8 - - + -
241H ASN* 3.9 17.3 - - + +
242H HIS 3.3 10.8 - - - +
243H THR* 2.7 28.8 + - - +
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Residues in contact with CYS 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H TRP* 3.8 15.5 - - - -
179H CYS* 2.5 40.6 - - - -
189H MET* 3.9 9.6 - - + -
190H ARG 3.3 5.2 - - - +
191H TRP* 3.4 32.6 - - + -
230H THR* 1.3 73.2 - - - +
232H VAL* 1.3 60.7 + - - +
240H ILE 3.9 0.3 - - - +
241H ASN* 3.1 21.8 - - - +
242H HIS* 3.0 16.2 + - - -
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Residues in contact with VAL 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H THR 3.6 0.9 - - - +
189H MET* 3.4 3.5 - - - +
190H ARG* 2.7 74.7 + - + +
192H LEU* 4.0 24.2 - - + -
230H THR* 3.9 15.9 - - + -
231H CYS* 1.3 77.0 - - - +
233H VAL* 1.3 63.4 + - - +
234H GLU* 4.7 1.8 - - - +
239H SER* 4.1 17.3 - - - +
240H ILE 3.7 6.5 - - - +
241H ASN* 4.3 7.6 - - + -
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Residues in contact with VAL 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H PRO* 3.7 10.6 - - + +
156H TRP* 3.5 27.4 - - + -
181H ALA* 3.9 12.8 - - + -
187H PRO* 3.3 31.0 - - + -
188H THR 3.1 8.7 - - - +
189H MET* 3.5 32.5 - - + -
214H TRP* 4.5 1.8 - - + -
232H VAL* 1.3 74.7 - - - +
234H GLU* 1.3 68.3 + - - +
239H SER* 3.3 1.4 + - - -
240H ILE* 2.9 39.9 + - + +
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Residues in contact with GLU 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H PRO* 3.5 4.5 - - - -
187H PRO* 3.0 6.5 - - - +
188H THR* 2.8 49.5 + - - +
190H ARG* 3.6 24.1 + - - +
232H VAL* 4.7 0.8 - - - +
233H VAL* 1.3 80.2 - - - +
235H ASN* 1.3 68.5 + - - +
238H GLY 3.2 15.3 - - - +
239H SER* 3.2 17.9 + - - +
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Residues in contact with ASN 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ARG 3.0 24.2 + - - -
153H ALA 3.9 0.2 - - - -
154H PRO* 3.2 25.5 - - - +
183H GLY* 4.1 2.4 - - - -
184H ASN 4.0 2.8 - - - +
185H PRO* 3.1 36.5 + - + +
186H MET 4.8 1.1 - - - +
187H PRO* 4.1 3.9 - - + +
234H GLU* 1.3 82.7 - - - +
236H GLU* 1.3 60.1 + - - +
237H TYR* 2.8 27.1 + - - +
238H GLY 2.9 18.3 + - - +
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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