Contacts of the strand formed by residues 215 - 220 (chain D) in PDB entry 1XU2
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 ILE 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D ILE* 3.7 45.1 - - + -
146D VAL 3.5 3.1 - - - -
147D ARG* 3.3 32.1 - - - +
174D SER 3.6 0.9 - - - +
175D ARG* 3.3 3.3 - - - -
176D GLU* 2.8 55.9 + - + +
213D GLY 4.3 3.1 - - - +
214D ASP* 1.3 73.6 - - - +
216D ILE* 1.3 63.9 + - - +
217D THR* 4.0 11.1 + - + +
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Residues in contact with ILE 216 (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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144D ASP 4.5 0.2 - - - +
145D ILE* 3.4 6.9 - - - -
146D VAL* 2.8 50.0 + - + +
148D VAL* 4.2 15.7 - - + -
156D LEU* 4.2 6.3 - - + -
173D VAL* 4.0 21.3 - - + -
174D SER 3.2 7.2 - - - +
175D ARG* 3.9 23.1 - - + -
184D LEU* 4.6 2.7 - - + -
210D LEU* 4.0 22.4 - - + -
214D ASP* 4.7 1.8 - - + -
215D ILE* 1.3 78.3 - - - +
217D THR* 1.3 64.4 + - - +
218D VAL* 5.3 3.4 - - + -
236D LEU* 5.5 1.8 - - + -
238D PHE* 4.1 29.2 - - + -
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Residues in contact with THR 217 (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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126D GLU* 4.6 4.5 - - - +
144D ASP 4.7 4.5 - - - -
145D ILE* 3.8 22.0 - - + -
172D VAL 3.5 1.0 + - - +
173D VAL* 3.2 7.1 - - - +
174D SER* 2.9 48.6 + - - -
176D GLU* 3.7 22.7 + - - +
215D ILE* 4.1 6.7 + - + +
216D ILE* 1.3 76.3 - - - +
218D VAL* 1.3 64.8 + - - +
219D LYS* 4.1 28.7 - - - +
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Residues in contact with VAL 218 (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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125D THR 4.3 0.2 - - - +
126D GLU* 3.8 22.7 + - - +
127D VAL* 4.4 5.7 + - + -
129D TRP* 4.3 22.0 + - + +
144D ASP 4.7 7.1 + - - +
158D SER* 4.1 11.0 - - - +
160D VAL* 4.7 5.2 - - + -
171D GLN* 4.0 24.2 - - + -
172D VAL 3.5 2.7 - - - -
173D VAL* 4.0 14.1 - - + -
216D ILE* 5.3 1.6 - - + -
217D THR* 1.3 78.0 - - - +
219D LYS* 1.3 62.8 + - - +
220D ILE* 4.4 8.8 - - + +
236D LEU* 3.9 39.0 - - + -
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Residues in contact with LYS 219 (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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124D VAL* 3.9 22.6 - - + +
125D THR 3.8 3.6 - - - -
126D GLU* 3.7 31.9 - - + +
171D GLN* 3.4 0.5 - - - -
172D VAL* 2.9 42.1 + - + +
176D GLU* 4.9 6.9 + - - -
181D ARG* 3.5 31.2 - - - +
217D THR* 4.3 23.1 - - - +
218D VAL* 1.3 76.8 - - - +
220D ILE* 1.3 64.2 + - - +
221D PRO* 3.4 8.7 - - + +
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Residues in contact with ILE 220 (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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124D VAL* 3.4 1.4 - - - -
125D THR* 2.9 42.7 + - - +
127D VAL* 4.8 8.3 - - + -
160D VAL* 4.5 6.7 - - + -
162D PHE* 3.9 15.5 - - + -
169D MET* 3.8 16.6 - - + -
170D GLY 3.5 19.7 - - - +
171D GLN* 4.2 11.2 - - + -
218D VAL* 4.4 11.0 - - + +
219D LYS* 1.3 77.6 - - - +
221D PRO* 1.3 57.3 - - + +
222D ARG* 2.7 20.0 + - - +
225D ALA* 3.6 24.2 - - + -
227D LEU* 4.0 17.9 - - + -
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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