Contacts of the strand formed by residues 168 - 176 (chain D) in PDB entry 1XU1
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 THR 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG 4.0 17.5 - - - +
199A TYR* 4.3 20.9 - - + +
166D THR* 3.7 4.1 - - - +
167D PHE* 1.3 105.6 - - + +
169D MET* 1.3 68.8 + - - +
188D ILE* 4.4 4.9 - - + -
189D ARG 3.3 7.4 - - - +
190D SER* 4.2 7.2 - - - -
222D ARG* 2.9 47.4 + - - -
82T LEU* 4.8 0.4 - - - -
83T LEU* 3.7 14.2 - - + +
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Residues in contact with MET 169 (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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162D PHE* 3.6 38.8 - - + -
164D ASP* 3.6 24.0 - - + +
166D THR* 3.6 20.9 - - - +
168D THR* 1.3 82.0 - - - +
170D GLY* 1.3 59.6 + - - +
188D ILE* 3.6 2.6 - - - +
189D ARG* 2.9 32.6 + - - +
191D MET* 4.0 21.0 - - + +
220D ILE* 3.9 7.6 - - + -
222D ARG* 3.6 17.0 - - + +
225D ALA* 3.6 30.7 - - + -
226D LYS 4.6 0.2 - - - +
82T LEU* 3.5 9.3 - - - +
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Residues in contact with GLY 170 (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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162D PHE* 3.4 17.3 - - - -
169D MET* 1.3 78.3 - - - +
171D GLN* 1.3 63.9 + - - +
187D CYS 3.1 15.7 - - - -
202D CYS* 4.5 1.6 - - - -
220D ILE* 3.4 27.2 - - - +
221D PRO* 3.7 5.2 - - - +
82T LEU* 3.5 10.4 - - - +
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Residues in contact with GLN 171 (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 SER* 3.3 36.0 + - - +
160D VAL* 3.6 27.9 - - + +
162D PHE* 4.0 0.2 - - - -
170D GLY* 1.3 76.1 - - - +
172D VAL* 1.3 65.9 + - - +
173D VAL* 4.5 7.4 - - + -
185D PHE* 4.2 2.3 - - + +
186D ARG* 3.3 5.5 - - - +
187D CYS* 3.1 42.2 + - + +
202D CYS* 3.0 39.3 + - - +
204D SER* 4.6 1.6 - - - +
218D VAL* 4.2 12.3 - - + -
219D LYS 3.5 9.0 - - - +
220D ILE* 4.3 4.7 - - + -
82T LEU* 4.1 1.1 - - - +
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Residues in contact with VAL 172 (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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171D GLN* 1.3 77.7 - - - +
173D VAL* 1.3 64.1 + - - +
174D SER* 3.7 12.0 + - - +
183D THR* 3.7 25.6 - - + -
185D PHE 3.8 2.9 - - - -
186D ARG* 4.1 12.1 - - + -
217D THR* 3.6 1.9 + - - +
218D VAL* 3.6 1.9 - - - -
219D LYS* 2.9 36.5 + - + +
221D PRO* 3.6 28.5 - - + -
81T HIS 4.5 7.4 - - - +
82T LEU* 3.8 10.3 - - + -
84T ARG* 4.0 11.4 - - - +
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Residues in contact with VAL 173 (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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156D LEU* 4.1 16.2 - - + -
158D SER* 4.1 11.0 - - - +
171D GLN* 4.5 5.8 - - + -
172D VAL* 1.3 75.6 - - - +
174D SER* 1.3 66.0 + - - +
183D THR* 3.7 1.7 - - - +
184D LEU* 2.8 26.8 + - + -
185D PHE* 2.9 55.8 + - + +
216D ILE* 4.1 18.6 - - + -
217D THR 3.3 8.7 - - - +
218D VAL* 4.0 20.9 - - + -
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Residues in contact with SER 174 (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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172D VAL* 3.7 15.6 + - - +
173D VAL* 1.3 77.5 + - - +
175D ARG* 1.3 63.3 + - - +
176D GLU* 5.7 0.7 - - - -
181D ARG* 4.4 21.7 + - - -
182D GLU 3.3 12.8 - - - -
183D THR* 3.7 12.8 + - - -
184D LEU* 4.1 5.8 - - - +
215D ILE 3.8 0.2 - - - +
216D ILE* 3.3 10.0 - - - +
217D THR* 3.0 44.1 + - - -
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Residues in contact with ARG 175 (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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174D SER* 1.3 74.2 - - - +
176D GLU* 1.3 62.6 + - - +
177D GLY* 4.2 18.2 + - - +
178D GLN* 5.2 4.0 - - - +
180D ARG* 3.9 7.3 + - - +
181D ARG* 3.6 1.7 - - - +
182D GLU* 2.8 73.9 + - - +
184D LEU* 4.2 13.0 - - + +
209D HIS 4.1 9.7 + - - -
210D LEU* 3.9 16.6 - - - -
211D HIS* 4.4 14.1 - - - -
214D ASP* 2.9 46.0 + - + +
215D ILE 3.5 3.8 - - - -
216D ILE* 4.0 11.0 - - + -
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Residues in contact with GLU 176 (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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174D SER* 5.9 0.7 - - - -
175D ARG* 1.3 75.1 - - - +
177D GLY* 1.3 59.0 + - - +
180D ARG 3.4 9.2 - - - +
181D ARG* 3.0 46.4 + - + +
213D GLY 4.3 1.7 - - - +
214D ASP* 3.4 5.8 - - - -
215D ILE* 2.8 56.5 + - + +
217D THR* 3.9 19.5 + - + +
219D LYS* 4.6 2.1 + - - -
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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