Contacts of the strand formed by residues 179 - 185 (chain D) in PDB entry 3UX9
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 LEU 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D TYR* 5.2 1.1 - - + -
41D GLN* 4.7 1.3 - - - +
47D PRO* 3.7 33.9 - - + -
90D TYR* 3.4 36.4 - - + -
103D PHE* 3.7 51.4 - - + +
104D GLY 4.5 3.6 - - - +
171D VAL* 4.2 14.1 - - + -
172D ARG 3.7 2.2 - - - +
173D GLN* 3.7 30.7 - - + +
178D GLY* 1.3 74.5 - - - +
180D GLU* 1.3 59.6 + - - +
229D TYR* 4.7 6.5 - - + -
243D TRP* 4.2 4.9 - - + -
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Residues in contact with GLU 180 (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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103D PHE* 4.6 1.3 - - - +
171D VAL* 3.5 4.2 - - - +
172D ARG* 2.9 76.5 + - + +
178D GLY 4.6 3.4 - - - +
179D LEU* 1.3 75.5 - - - +
181D TRP* 1.3 72.8 + - - +
182D VAL* 3.6 1.7 - - + +
195D ALA* 4.7 2.4 - - - +
197D SER* 3.3 22.1 + - - -
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Residues in contact with TRP 181 (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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100D GLU* 3.7 20.2 - - + -
101D TRP* 3.3 59.5 - + + +
102D VAL* 5.0 0.8 - - - +
103D PHE* 3.9 22.2 - - + +
169D SER* 4.2 1.3 - - - -
170D TRP 3.8 8.5 - - - -
171D VAL* 4.2 13.0 - - + -
180D GLU* 1.3 84.9 - - - +
182D VAL* 1.3 60.9 + - - +
183D SER 2.8 38.5 + - - -
184D ALA* 3.4 7.1 - - + +
193D TYR* 3.6 12.1 - - + -
194D TYR* 3.5 21.8 - - - -
195D ALA* 3.5 36.9 - - + +
233D TYR* 3.2 24.4 + - - -
240D MET* 5.0 2.5 - - + -
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Residues in contact with VAL 182 (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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170D TRP* 3.2 14.4 + - + +
171D VAL* 4.3 0.7 - - - -
172D ARG* 3.5 42.2 - - + +
180D GLU* 3.6 12.6 - - + +
181D TRP* 1.3 79.4 - - - +
183D SER* 1.3 71.2 + - - +
194D TYR* 3.4 1.6 - - - -
195D ALA* 2.8 31.9 + - - +
198D VAL* 3.8 11.6 - - + +
202D PHE* 3.9 29.4 - - + -
215D LEU* 4.5 10.8 - - + -
228D TYR* 4.6 4.3 - - + -
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Residues in contact with SER 183 (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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169D SER* 3.4 1.0 - - - -
170D TRP* 3.1 22.7 + - - -
181D TRP* 2.8 18.7 + - - -
182D VAL* 1.3 90.0 - - - +
184D ALA* 1.3 62.3 + - - +
193D TYR 3.2 11.2 + - - -
194D TYR* 3.7 11.9 - - - -
204D ILE* 3.0 41.0 - - - +
215D LEU* 4.6 7.6 - - - -
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Residues in contact with ALA 184 (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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30C LEU* 5.1 2.0 - - + -
101D TRP* 3.8 16.6 - - + -
168D MET 3.4 6.5 - - - -
181D TRP* 3.6 15.9 - - + +
183D SER* 1.3 76.2 + - - +
185D ILE* 1.3 64.4 + - - +
192D THR* 3.4 3.3 - - - -
193D TYR* 2.9 31.8 + - + +
204D ILE* 3.6 8.0 - - - +
233D TYR* 3.7 24.2 - - + -
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Residues in contact with ILE 185 (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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30C LEU* 4.1 4.9 - - - +
167D ALA* 3.4 2.9 - - - +
168D MET* 3.0 27.3 + - + +
184D ALA* 1.3 76.4 - - - +
186D SER* 1.3 73.4 + - - +
189D GLY* 4.0 18.2 - - - +
191D SER 3.4 11.9 - - - +
192D THR* 4.1 5.2 - - + -
204D ILE* 3.5 33.9 - - + +
205D SER* 3.8 12.6 - - - -
206D ARG* 3.5 35.8 + - + +
213D LEU* 3.6 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