Contacts of the strand formed by residues 171 - 185 (chain D) in PDB entry 3U8M
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 PHE 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.6 40.8 - - + -
39D LEU 4.8 1.8 - - - -
41D VAL* 3.4 37.0 - - + -
128D VAL* 4.0 10.5 - - + -
165D PHE* 3.5 15.4 - - - -
166D SER 4.8 1.0 - - - +
169D SER* 3.0 10.2 + - - +
170D ARG* 1.3 119.3 - - + +
172D GLU* 1.3 61.6 + - - +
201D PHE* 4.0 18.4 - + + -
202D ARG 3.5 19.1 - - - +
203D LYS* 4.0 26.5 - - + -
204D LYS* 3.2 15.8 - - - +
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Residues in contact with GLU 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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165D PHE* 4.1 7.0 - - - -
171D PHE* 1.3 76.7 - - - +
173D ILE* 1.3 64.1 + - - +
174D LEU* 3.8 7.3 + - + -
201D PHE* 3.3 7.8 - - - +
202D ARG* 2.9 72.8 + - + +
203D LYS 4.2 3.5 - - - +
204D LYS* 3.7 24.8 - - + +
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Residues in contact with ILE 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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35D PHE* 3.7 18.4 - - + -
38D ILE* 4.8 4.0 - - + -
161D ASP* 3.5 43.8 - - + +
162D SER* 3.5 18.0 + - - +
165D PHE* 3.4 42.6 - - + -
172D GLU* 1.3 78.1 - - - +
174D LEU* 1.3 66.4 + - - +
175D ASP 3.7 11.4 - - - +
176D VAL* 3.9 9.0 - - + -
199D LEU* 4.1 16.4 - - + -
200D ASN 3.9 3.6 - - - +
201D PHE* 4.4 0.9 - - + -
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Residues in contact with LEU 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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131D GLU 3.8 6.7 - - - +
132D SER* 3.3 28.3 - - - +
133D GLY* 4.2 3.1 - - - -
161D ASP* 4.0 6.4 - - - +
172D GLU* 4.5 8.5 - - + +
173D ILE* 1.3 79.2 - - - +
175D ASP* 1.3 63.1 + - + +
200D ASN* 2.7 28.0 + - - +
201D PHE* 4.3 6.1 - - - -
202D ARG* 3.6 53.6 - - + +
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Residues in contact with ASP 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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161D ASP* 3.8 13.9 - - - +
173D ILE* 3.6 2.6 - - - +
174D LEU* 1.3 83.3 - - - +
176D VAL* 1.3 77.8 + - - +
177D THR* 3.6 22.6 - - + +
198D SER 4.4 0.4 - - - -
200D ASN* 2.9 42.9 + - + +
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Residues in contact with VAL 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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33D LEU 5.2 3.1 - - - +
35D PHE* 4.2 14.4 - - + -
161D ASP* 3.4 40.1 + - + +
173D ILE* 3.9 8.5 - - + -
175D ASP* 1.3 86.4 + - - +
177D THR* 1.3 68.1 + - - +
178D GLN* 4.5 12.0 - - + +
197D VAL* 3.7 28.9 - - + -
198D SER 3.4 6.5 - - - +
199D LEU* 4.0 13.5 - - + -
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Residues in contact with THR 177 (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 ASP* 3.6 20.4 - - - +
176D VAL* 1.3 76.9 - - - +
178D GLN* 1.3 65.9 + - - +
179D LYS 4.3 0.2 - - - -
196D GLU 3.7 0.5 - - - +
197D VAL* 3.5 3.1 - - - +
198D SER* 2.7 50.1 + - - -
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Residues in contact with GLN 178 (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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31D VAL 3.6 9.2 - - - +
32D SER* 4.2 8.0 + - - +
33D LEU 3.9 22.4 + - - +
154D PRO* 3.3 41.9 - - + +
155D THR 4.0 5.1 + - - -
176D VAL* 4.5 9.3 - - + +
177D THR* 1.3 84.9 - - - +
179D LYS* 1.3 61.3 + - - +
195D VAL* 4.4 5.2 - - + +
196D GLU 3.4 5.6 - - - +
197D VAL* 3.8 28.5 - - + +
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Residues in contact with LYS 179 (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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154D PRO* 4.9 0.7 - - - -
178D GLN* 1.3 75.0 - - - +
180D LYS* 1.3 66.4 + - - +
181D ASN* 3.3 25.1 + - - +
195D VAL* 3.4 3.7 - - - -
196D GLU* 2.5 60.7 + - + +
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Residues in contact with LYS 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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152D VAL* 3.0 23.1 - - + +
153D ASP* 3.6 14.8 - - - +
154D PRO* 4.2 20.1 - - + +
179D LYS* 1.3 78.3 - - - +
181D ASN* 1.3 93.2 + - - +
182D SER* 4.2 7.5 - - - +
193D GLU* 3.1 35.1 + - - -
194D ASP 3.6 9.6 - - - +
195D VAL* 4.4 1.3 - - + +
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Residues in contact with ASN 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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179D LYS* 3.3 37.2 + - - +
180D LYS* 1.3 84.0 + - - +
182D SER* 1.3 62.2 + - - +
183D VAL* 4.1 8.7 - - + +
193D GLU* 3.3 4.3 - - - -
194D ASP* 2.5 64.6 + - - +
196D GLU* 3.3 29.4 + - - +
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Residues in contact with SER 182 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D SER* 5.0 1.9 - - - -
180D LYS* 4.2 10.5 - - - -
181D ASN* 1.3 77.9 - - - +
183D VAL* 1.3 62.7 + - - +
184D THR* 5.7 0.5 - - - +
191D ALA* 3.8 21.0 - - - +
192D TYR 3.9 3.8 - - - -
193D GLU* 4.4 12.2 + - - +
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Residues in contact with VAL 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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139D LYS* 4.9 6.7 - - - +
181D ASN* 4.3 8.1 - - + -
182D SER* 1.3 82.1 + - - +
184D THR* 1.3 78.3 + - - +
185D TYR* 3.2 32.9 - - + +
191D ALA* 4.3 1.1 - - - -
192D TYR 2.9 35.5 + - - +
194D ASP* 3.7 18.6 - - - +
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Residues in contact with THR 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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182D SER 5.7 0.4 - - - +
183D VAL* 1.3 89.8 - - - +
185D TYR* 1.3 71.9 + - - +
188D CYS 4.8 2.5 - - - -
189D PRO 4.9 5.8 - - - +
190D GLU 4.1 17.7 - - - +
191D ALA* 4.3 11.0 - - + -
163E GLU* 5.1 3.8 - - - +
164E TYR* 5.1 1.6 - - - -
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Residues in contact with TYR 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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89D TYR* 3.3 20.8 + + - -
139D LYS* 3.0 28.8 + - - -
183D VAL* 3.2 38.3 - - + +
184D THR* 1.3 78.8 - - - +
186D SER* 1.3 63.2 + - - +
187D CYS* 3.3 15.3 - - - +
188D CYS* 2.7 32.4 + - + +
190D GLU 4.7 1.2 + - - -
192D TYR* 4.1 27.0 + + + -
194D ASP* 4.5 1.9 + - - +
53E TRP* 3.6 36.1 - + + -
114E MET* 5.7 0.4 - - + -
163E GLU* 5.0 1.8 - - - -
164E TYR* 3.3 23.8 - + + +
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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