Contacts of the strand formed by residues 238 - 249 (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 238 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ALA* 4.1 2.0 - - - -
154H PRO* 3.5 12.6 - - - +
234H GLU* 3.2 4.0 - - - +
235H ASN* 2.9 33.1 + - - +
236H GLU 3.5 1.4 + - - -
237H TYR* 1.3 81.0 - - - +
239H SER* 1.3 61.2 + - - -
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Residues in contact with SER 239 (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* 4.4 0.9 - - - +
232H VAL* 4.1 11.4 - - - +
233H VAL 3.3 7.6 + - - -
234H GLU* 3.2 29.6 + - - +
238H GLY* 1.3 76.1 - - - -
240H ILE* 1.3 67.8 + - - +
241H ASN* 5.4 0.5 - - - +
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Residues in contact with ILE 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H PRO* 3.5 40.6 - - + +
155H TYR* 3.7 12.1 - - - +
156H TRP* 3.5 41.7 - - + +
231H CYS 3.9 0.2 - - - +
232H VAL* 3.7 3.3 - - - +
233H VAL* 2.9 38.0 + - + +
239H SER* 1.3 81.3 + - - +
241H ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H TRP* 3.8 12.0 + - - -
230H THR* 3.9 16.0 - - + +
231H CYS 3.1 14.8 - - - +
232H VAL* 4.3 10.8 - - + -
239H SER 5.4 0.5 - - - +
240H ILE* 1.3 78.2 - - - +
242H HIS* 1.3 66.4 + - - +
243H THR* 4.5 5.9 + - - +
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Residues in contact with HIS 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H TRP* 4.0 4.3 + - + -
162H MET* 3.4 47.9 + - + +
165H ARG* 3.9 27.0 + - + +
179H CYS* 4.2 0.8 - - - -
229H TYR 3.9 0.9 - - - +
230H THR* 3.3 2.3 - - - -
231H CYS* 3.0 36.5 + - - -
241H ASN* 1.3 78.0 + - - +
243H THR* 1.3 67.9 + - - +
244H TYR* 3.0 54.0 + + - -
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Residues in contact with THR 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H ARG* 3.6 25.8 - - - +
228H ASN* 3.8 24.7 - - + +
229H TYR 3.4 5.6 - - - +
230H THR* 2.7 27.7 + - - +
241H ASN* 4.5 6.8 + - - +
242H HIS* 1.3 80.4 + - - +
244H TYR* 1.3 75.4 + - - +
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Residues in contact with TYR 244 (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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161H LYS 3.7 5.1 + - - -
162H MET* 3.3 25.7 - - - +
164H LYS 3.6 25.8 - - - -
165H ARG* 3.3 8.1 - - - +
167H HIS* 4.2 8.3 - + - -
177H PHE* 3.2 41.3 - + + -
178H ARG 2.4 43.8 + - - -
179H CYS* 3.9 7.6 - - - -
191H TRP* 4.3 9.0 - + - -
228H ASN* 3.4 3.8 - - - -
229H TYR* 2.7 34.4 + - - +
242H HIS* 3.0 33.7 - + - -
243H THR* 1.3 76.8 - - - +
245H HIS* 1.3 60.9 + - - +
246H LEU 4.1 0.2 - - - -
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Residues in contact with HIS 245 (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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165H ARG* 2.9 10.3 + - - +
166H LEU* 3.1 20.9 - - + +
167H HIS* 2.7 30.5 + - - +
177H PHE* 4.6 1.6 - - - -
227H GLY 3.6 5.2 - - - +
228H ASN* 3.9 14.4 - - - +
243H THR 4.4 0.2 + - - -
244H TYR* 1.3 74.2 - - - +
246H LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 246 (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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166H LEU* 4.7 0.4 - - - -
167H HIS* 3.4 13.2 - - + +
169H VAL* 4.5 3.1 - - + -
175H VAL* 3.9 26.0 - - + -
177H PHE* 4.0 5.2 - - + -
218H MET* 3.8 28.0 - - + -
221H VAL* 4.6 9.6 - - + -
225H ASP* 3.6 32.3 - - + +
226H LYS* 3.3 8.4 - - - +
227H GLY 2.8 26.4 + - - -
229H TYR* 3.7 17.7 - - + -
244H TYR 4.1 0.6 + - - -
245H HIS* 1.3 74.4 - - - +
247H ASP* 1.3 75.9 + - - +
248H VAL* 4.5 9.6 - - + -
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Residues in contact with ASP 247 (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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151D MET* 3.5 31.3 - - + +
166H LEU* 4.3 13.4 - - + +
167H HIS 2.9 11.6 + - - +
168H ALA* 3.1 5.7 - - + +
169H VAL 3.0 25.5 + - - -
226H LYS* 3.3 38.6 + - - +
246H LEU* 1.3 77.8 - - - +
248H VAL* 1.3 71.1 + - - +
249H VAL* 4.2 1.1 + - - +
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Residues in contact with VAL 248 (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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169H VAL* 3.4 4.3 - - + +
171H ALA* 3.4 37.2 - - + +
221H VAL* 3.9 22.4 - - + -
222H VAL* 3.3 37.0 - - - +
223H PRO* 3.7 17.0 - - + +
225H ASP* 4.6 1.8 - - + -
226H LYS* 4.9 5.3 - - - +
246H LEU* 4.5 14.1 - - + -
247H ASP* 1.3 83.1 + - - +
249H VAL* 1.3 69.1 + - - +
250H GLU 4.4 0.3 + - - -
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Residues in contact with VAL 249 (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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149D LEU* 3.9 29.4 - - + -
150D PRO 4.0 15.7 - - - +
151D MET* 4.2 28.9 - - + -
169H VAL 3.0 6.3 + - - -
170H PRO* 3.1 9.0 - - - +
171H ALA 2.7 28.0 + - - -
247H ASP* 4.9 1.3 - - - +
248H VAL* 1.3 80.6 - - - +
250H GLU* 1.3 65.1 + - - +
251H ARG* 3.6 16.9 + - - +
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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