Contacts of the strand formed by residues 215 - 220 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.8 36.3 - - + -
146A VAL 3.6 3.6 - - - -
147A ARG* 3.7 36.6 - - + +
175A ARG* 3.2 5.0 - - - -
176A GLU* 2.9 50.6 + - + +
177A GLY* 6.0 0.4 - - - -
213A GLY 4.3 7.4 - - - +
214A ASP* 1.3 76.6 - - - +
216A ILE* 1.3 64.7 + - - +
217A THR* 4.0 9.3 + - + -
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Residues in contact with ILE 216 (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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145A ILE* 3.4 9.7 - - - +
146A VAL* 2.9 40.7 + - + +
148A VAL* 4.0 20.6 - - + -
156A LEU* 4.1 8.7 - - + -
173A VAL* 4.0 21.5 - - + -
174A SER 3.2 7.4 - - - +
175A ARG* 3.5 28.7 - - + -
184A LEU* 4.6 3.4 - - + -
210A LEU* 4.0 21.1 - - + -
214A ASP* 4.8 1.6 - - + -
215A ILE* 1.3 74.6 - - - +
217A THR* 1.3 66.3 + - - +
218A VAL* 5.0 5.2 - - + -
236A LEU* 5.5 0.9 - - + -
238A PHE* 4.3 22.2 - - + -
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Residues in contact with THR 217 (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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126A GLU* 5.0 2.0 - - - +
144A ASP 4.9 1.1 - - - -
145A ILE* 3.8 21.1 - - + -
172A VAL 3.5 1.1 + - - +
173A VAL* 3.3 7.6 - - - +
174A SER* 3.0 48.5 + - - +
176A GLU* 3.7 24.2 + - + +
215A ILE* 4.1 8.3 - - + -
216A ILE* 1.3 77.6 - - - +
218A VAL* 1.3 64.4 + - - +
219A LYS* 4.0 28.3 - - - +
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Residues in contact with VAL 218 (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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126A GLU* 3.5 24.7 + - - +
127A VAL* 4.6 3.8 + - + -
129A TRP* 4.5 22.2 + - + +
144A ASP 4.7 6.9 + - - +
158A SER* 4.1 15.7 - - - +
160A VAL* 4.9 6.1 - - + -
171A GLN* 4.2 17.9 - - + -
172A VAL 3.5 3.4 - - - -
173A VAL* 4.1 15.3 - - + -
216A ILE* 5.0 2.7 - - + +
217A THR* 1.3 77.6 - - - +
219A LYS* 1.3 63.1 + - - +
220A ILE* 4.4 6.4 + - + +
236A LEU* 3.9 38.4 - - + -
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Residues in contact with LYS 219 (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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124A VAL* 4.3 24.0 - - + +
125A THR 3.7 3.4 - - - -
126A GLU* 3.7 27.8 - - + +
171A GLN* 3.3 2.4 - - - -
172A VAL* 2.8 41.5 + - + +
174A SER* 6.1 0.4 - - - +
176A GLU* 4.3 12.3 + - - -
181A ARG* 6.3 1.0 - - - +
217A THR* 4.0 26.0 - - - +
218A VAL* 1.3 79.6 - - - +
220A ILE* 1.3 64.1 + - - +
221A PRO* 3.4 8.0 - - + +
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Residues in contact with ILE 220 (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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124A VAL* 3.5 1.2 - - - -
125A THR* 2.8 50.8 + - - +
127A VAL* 4.6 11.9 - - + -
160A VAL* 4.6 9.6 - - + -
162A PHE* 3.9 16.2 - - + -
169A MET* 3.8 16.4 - - + -
170A GLY 3.5 19.5 - - - +
171A GLN* 4.4 9.0 - - + -
218A VAL* 4.9 5.8 - - + +
219A LYS* 1.3 76.2 - - - +
221A PRO* 1.3 55.1 - - - +
222A ARG* 2.7 23.0 + - - +
225A ALA* 3.7 22.9 - - + -
227A LEU* 4.1 18.6 - - + -
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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