Contacts of the strand formed by residues 176 - 188 (chain D) in PDB entry 6UWZ
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 TRP 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.8 27.6 - - + -
42D SER 6.1 0.2 - - - -
43D VAL* 3.7 34.5 - - + +
45D GLU* 4.0 1.1 + - + -
138D ASP* 4.0 7.9 - - - -
140D GLN* 3.8 26.7 - - + -
170D PHE* 5.8 2.6 - - - -
173D SER* 3.7 24.4 + - - -
174D GLY 3.8 1.3 + - - -
175D GLU* 1.3 102.8 + - + +
177D VAL* 1.3 65.9 + - - +
178D MET* 4.1 4.5 + - + +
207D MET* 3.5 30.3 - - + -
208D GLN 3.4 4.7 - - - -
209D ARG* 3.2 70.4 - - + +
210D ILE* 4.0 3.0 - - - +
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Residues in contact with VAL 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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176D TRP* 1.3 76.5 - - - +
178D MET* 1.3 70.8 + - - +
179D LYS* 3.3 13.7 + - + +
207D MET* 3.1 6.0 - - - -
208D GLN* 2.7 48.7 + - + +
210D ILE* 3.9 23.6 - - + -
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Residues in contact with MET 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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37D LEU* 4.6 8.3 - - + -
40D LEU* 4.9 8.3 - - + -
167D LEU* 4.0 25.1 - - + -
170D PHE* 3.9 32.3 - - + -
176D TRP* 4.1 4.5 + - + +
177D VAL* 1.3 76.1 - - - +
179D LYS* 1.3 64.8 + - - +
180D ASP 4.3 2.5 - - - +
181D TYR* 4.1 17.5 - - + -
205D PHE* 3.6 28.0 - - + -
206D ILE 3.6 11.7 - - - +
207D MET* 3.9 28.7 - - + -
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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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139D GLN* 2.3 34.1 + - - +
177D VAL* 3.3 9.1 + - + +
178D MET* 1.3 76.9 - - - +
180D ASP* 1.3 61.2 + - + +
181D TYR* 4.9 5.0 - - - -
206D ILE* 2.9 20.4 + - + +
208D GLN* 3.4 46.2 + - + +
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Residues in contact with ASP 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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164D ARG* 3.4 25.0 + - - +
178D MET* 4.3 2.1 - - - +
179D LYS* 1.3 81.2 - - + +
181D TYR* 1.3 70.3 + - - +
182D ARG* 4.9 4.9 - - - +
204D HIS* 4.4 13.1 - - + -
205D PHE 3.7 0.2 - - - -
206D ILE* 2.8 53.1 + - + +
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Residues in contact with TYR 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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164D ARG* 3.1 45.4 + - + +
165D PRO* 3.7 31.2 - - + -
167D LEU* 3.7 45.3 + - + +
178D MET* 4.1 12.6 - - + -
179D LYS 4.9 5.6 - - - -
180D ASP* 1.3 83.8 + - - +
182D ARG* 1.3 62.1 + - - +
204D HIS* 3.4 7.4 - - - -
205D PHE* 3.5 26.2 - - + -
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Residues in contact with ARG 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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163D ASP* 3.2 46.7 + - - +
164D ARG* 4.0 21.9 - - + +
165D PRO* 3.7 11.6 - - - +
180D ASP* 4.9 5.4 - - - +
181D TYR* 1.3 77.7 - - - +
183D GLY* 1.3 69.8 + - - +
184D TRP* 3.0 52.9 - - - +
203D TYR* 3.5 1.4 - - - -
204D HIS* 2.9 53.1 + - + +
2K NAG 5.4 0.4 - - - -
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Residues in contact with GLY 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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160D PRO* 5.1 6.3 - - - +
162D SER 4.6 2.3 - - - +
163D ASP* 2.9 29.5 + - - +
165D PRO* 4.0 1.6 - - - +
182D ARG* 1.3 79.3 + - - +
184D TRP* 1.3 67.0 + - - -
185D LYS 4.3 0.5 + - - -
201D ILE* 5.0 2.5 - - - -
202D THR 3.6 3.4 - - - -
203D TYR* 3.5 26.9 - - - -
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Residues in contact with TRP 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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160D PRO* 5.4 0.2 - - - -
182D ARG* 3.0 49.4 - - + +
183D GLY* 1.3 77.4 - - - -
185D LYS* 1.3 60.6 + - - +
186D HIS* 3.6 26.3 - + + +
201D ILE* 3.4 5.1 - - - -
202D THR 2.8 32.4 + - - -
204D HIS* 4.3 16.6 + + - -
2K NAG 3.1 52.8 + - - +
3K BMA 3.8 27.6 - - - -
5K MAN 3.8 23.6 - - - -
8K MAN 4.1 25.8 - - - -
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Residues in contact with LYS 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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157D SER* 4.2 7.7 + - - -
158D ILE 3.2 27.9 + - - +
159D SER* 3.7 12.9 + - - -
160D PRO* 4.0 29.0 - - + +
183D GLY 4.3 0.8 + - - -
184D TRP* 1.3 74.9 - - - +
186D HIS* 1.3 67.3 + - - +
187D TRP* 4.6 15.1 - - + -
199D LEU* 3.9 27.1 - - + +
200D ASP 3.4 11.2 - - - +
201D ILE* 4.2 7.0 - - + -
3K BMA 3.7 2.8 - - - -
7K MAN 3.2 22.7 - - - +
8K MAN 4.2 29.2 + - - +
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Residues in contact with HIS 186 (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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184D TRP* 3.6 23.8 - - + +
185D LYS* 1.3 79.7 + - - +
187D TRP* 1.3 61.3 + - - +
188D VAL* 5.1 2.5 - - + -
199D LEU* 3.3 6.1 - - - +
200D ASP* 2.8 61.4 + - - +
202D THR* 3.4 10.6 + - - -
2K NAG 2.7 61.7 + - + +
3K BMA 4.1 1.8 - - - -
7K MAN 3.3 11.5 - - - +
10K MAN 3.3 23.8 + - - +
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Residues in contact with TRP 187 (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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185D LYS* 4.6 18.6 - - + -
186D HIS* 1.3 74.7 - - - +
188D VAL* 1.3 62.6 + - - +
189D TYR* 3.8 13.9 - + - -
197D PRO* 4.0 11.0 - - + -
198D TYR 3.8 3.6 - - - -
199D LEU* 3.5 18.2 - - + -
6G THR 2.8 27.1 + - - -
7G ALA 3.4 22.2 - - - -
8G THR* 3.6 13.2 + - - -
9G SER* 3.7 24.7 - - - -
7K MAN 3.0 41.5 + - - -
8K MAN 3.9 21.3 - - - -
9K MAN 3.7 15.5 - - - -
10K MAN 3.3 16.3 + - - +
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Residues in contact with VAL 188 (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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186D HIS* 5.1 3.8 - - + -
187D TRP* 1.3 80.9 - - - +
189D TYR* 1.3 72.9 + - - +
190D TYR* 3.6 30.3 - - + +
197D PRO* 3.5 4.6 - - - +
198D TYR* 2.9 42.4 + - + +
200D ASP* 4.3 13.0 - - - +
30G ASP* 5.7 0.2 - - - +
39G VAL* 4.1 17.7 - - + -
10K MAN 3.9 15.7 - - - +
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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