Contacts of the strand formed by residues 189 - 195 (chain D) in PDB entry 2HU4
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 TRP 189 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 3.4 39.9 - - - -
124D CYS 3.9 6.5 - - - -
125D SER* 4.1 18.1 + - - -
128D GLU* 4.6 7.2 + - + +
130D ARG* 4.0 25.8 - - + +
132D PHE* 3.6 26.5 - + + -
172D ARG* 3.8 27.4 - - - +
174D GLU* 5.7 2.0 - - - +
183D CYS* 3.4 24.9 - - - -
184D HIS* 3.4 36.6 + + - -
188D SER* 1.3 75.0 - - - +
190D LEU* 1.3 61.8 + - - +
191D THR* 4.9 8.9 - - + +
206D LYS 3.4 1.4 - - - +
207D TYR* 3.4 5.6 - - - -
208D ASN* 2.9 30.2 + - - +
209D GLY 4.8 0.4 + - - +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ALA* 3.2 7.6 - - - +
183D CYS* 2.9 42.3 + - - +
185D ASP 6.0 0.4 - - - +
188D SER 3.8 0.8 + - - +
189D TRP* 1.3 73.5 - - - +
191D THR* 1.3 68.3 + - - +
192D ILE* 4.6 5.6 - - + -
205D LEU* 4.3 9.6 - - + -
206D LYS 3.1 21.1 - - - +
207D TYR* 4.4 10.1 - - + -
230D CYS* 4.3 1.3 - - - -
237D CYS* 3.8 26.9 - - + -
257D MET* 3.6 35.2 - - + -
260D GLY* 3.6 29.2 - - - +
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 4.5 4.7 - - + -
158D LEU* 4.7 9.4 - - + -
174D GLU* 3.5 37.2 + - + +
175D SER* 4.7 3.3 - - - -
181D SER 3.8 4.7 - - - -
182D ALA* 4.4 9.6 - - + -
189D TRP* 4.9 9.2 - - + +
190D LEU* 1.3 80.0 - - - +
192D ILE* 1.3 63.9 + - - +
193D GLY 4.2 0.4 - - - -
204D VAL 3.4 1.3 + - - +
205D LEU* 3.1 5.7 - - - +
206D LYS* 2.7 66.7 + - - +
209D GLY 6.4 0.4 - - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LEU* 4.0 2.6 - - - +
180D ALA* 2.9 27.9 - - - +
181D SER* 2.9 38.0 + - - +
190D LEU* 4.6 7.0 - - + +
191D THR* 1.3 80.0 - - - +
193D GLY* 1.3 60.0 + - - +
194D ILE* 4.2 2.9 - - + -
203D ALA* 4.2 4.9 - - + -
204D VAL 3.7 2.2 - - - -
205D LEU* 3.4 28.5 - - + -
225D THR* 5.0 1.1 - - + -
230D CYS* 4.6 6.3 - - - -
239D THR* 3.9 14.4 - - + +
241D MET* 3.5 25.4 - - + -
257D MET* 3.4 31.9 - - + -
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Residues in contact with GLY 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D SER* 4.1 15.3 + - - -
176D VAL 4.0 3.8 - - - +
177D ALA* 3.3 20.6 - - - -
179D SER 3.8 0.2 - - - -
180D ALA* 4.3 1.3 - - - -
191D THR 4.2 0.2 - - - -
192D ILE* 1.3 73.8 - - - +
194D ILE* 1.3 63.2 + - - -
195D SER* 3.9 0.7 + - - -
202D VAL 3.6 2.3 - - - +
204D VAL* 2.9 41.2 + - - +
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Residues in contact with ILE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ALA* 3.2 1.0 - - - +
178D TRP* 2.9 36.3 + - + -
179D SER* 2.9 18.5 + - - +
192D ILE* 4.8 1.1 - - + -
193D GLY* 1.3 73.5 - - - -
195D SER* 1.3 64.0 + - - +
201D ALA* 3.7 19.7 - - + -
202D VAL 3.5 9.2 - - - +
203D ALA* 3.9 16.6 - - + -
223D LEU* 3.3 36.1 - - + +
224D ARG* 3.6 24.9 - - - -
225D THR* 3.8 11.0 - - + +
241D MET* 3.9 18.4 - - + -
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 4.6 7.2 - - - -
456B TRP* 3.7 5.4 - - - -
458B TRP* 3.1 29.3 + - - -
153D SER 5.3 0.7 + - - -
154D PRO 5.4 0.2 + - - -
176D VAL* 3.6 27.2 - - - +
177D ALA* 4.4 1.6 - - - -
178D TRP* 3.5 13.7 + - - +
193D GLY 3.9 1.2 + - - -
194D ILE* 1.3 74.8 - - - +
196D GLY* 1.3 69.6 + - - +
201D ALA* 3.3 3.5 - - - -
202D VAL* 2.9 37.2 + - - +
204D VAL* 6.3 0.9 - - - -
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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