Contacts of the strand formed by residues 213 - 223 (chain B) 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 GLN 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B LYS* 5.4 0.3 + - - -
149B THR* 4.0 11.3 - - - +
150B ALA* 4.2 12.7 - - - +
153B TYR 4.5 3.3 - - - +
155B ALA* 3.6 25.6 + - + +
158B ILE* 2.7 32.2 + - - +
159B THR* 3.2 5.3 - - - +
160B MET* 3.2 43.4 - - - +
199B LYS* 4.1 16.9 - - - +
200B ASN 3.6 3.4 - - - -
202B TYR* 4.3 5.5 - - - -
210B THR* 4.4 12.0 - - - +
211B ASN* 4.3 3.3 - - - +
212B TYR* 1.3 84.0 - - + +
214B ASP* 1.3 69.9 + - - +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 2.9 45.6 - - - +
148B PHE 3.3 6.2 - - - +
149B THR* 3.2 11.4 - - - +
160B MET* 4.7 1.6 - - - -
199B LYS* 3.3 6.3 - - - +
200B ASN* 2.5 41.2 + - + +
202B TYR* 3.7 23.4 + - + +
213B GLN* 1.3 77.7 - - - +
215B VAL* 1.3 61.5 + - - +
216B THR* 2.0 33.1 + - - -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.0 18.6 - - + -
146B LEU 4.0 0.9 - - - +
148B PHE* 3.0 35.5 + - - +
160B MET* 3.8 43.2 - - + +
161B ASP 4.4 3.8 - - - +
162B LEU* 3.6 26.9 - - + -
198B LYS 3.2 4.7 - - - +
199B LYS* 4.5 9.2 - - + -
214B ASP* 1.3 75.5 - - - +
216B THR* 1.3 63.3 + - - +
217B PHE* 3.6 22.2 - - + -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER* 3.0 28.7 - - - +
146B LEU 3.4 8.7 - - - +
147B LYS* 4.1 5.7 - - + +
197B ALA* 3.3 2.6 - - - +
198B LYS 2.7 39.3 + - - +
200B ASN* 3.3 10.8 + - - -
202B TYR* 5.0 0.2 + - - -
214B ASP* 2.0 34.1 + - - -
215B VAL* 1.3 72.9 - - - +
217B PHE* 1.3 65.1 + - - +
218B TYR* 3.4 32.8 - - + +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.1 13.2 - - + -
36B SER* 4.0 13.2 - - - -
37B LEU* 3.6 41.3 - - + -
58B MET* 4.8 0.9 - - + -
145B SER* 3.6 0.9 - - - -
146B LEU* 2.8 46.2 + - + +
148B PHE* 3.6 33.0 - + - -
162B LEU* 4.7 2.5 - - + -
174B ILE 5.5 0.9 - - - -
176B TRP 4.9 3.8 - - - -
177B ILE* 3.9 23.6 - - + -
196B PRO 3.5 2.7 - - - -
197B ALA* 3.3 31.2 - - + -
215B VAL* 3.6 28.7 - - + -
216B THR* 1.3 73.5 - - - +
218B TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ASN* 4.2 17.5 - - - +
144B CYS 3.6 3.1 - - - -
145B SER* 4.0 15.3 - - - -
177B ILE* 3.8 4.4 - - - +
195B LYS* 3.3 9.5 - - - -
196B PRO* 2.9 44.3 + - + +
198B LYS* 3.8 10.0 - - + +
200B ASN* 3.1 14.2 + - - -
216B THR* 3.4 36.4 - - + +
217B PHE* 1.3 74.7 - - - +
219B LEU* 1.3 60.8 + - - +
220B ILE* 4.4 4.3 - - + -
486B PHE* 3.5 30.3 - + + -
1I NAG 3.7 30.7 - - - -
2I NAG 3.0 26.6 - - + +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.3 17.3 - - + -
42B LEU* 4.1 19.7 - - + -
52B LEU* 3.9 25.8 - - + -
54B SER* 5.6 0.4 - - - -
142B GLN 3.4 2.9 - - - +
143B ASN* 4.4 0.4 - - - -
144B CYS* 2.7 47.6 + - + +
146B LEU* 4.4 8.5 - - + -
177B ILE* 4.0 22.9 - - + -
179B ILE* 5.4 0.7 - - + -
192B ILE* 4.1 37.9 - - + -
194B HIS 3.9 0.4 - - - -
195B LYS* 4.3 4.5 - - + -
218B TYR* 1.3 73.0 - - - +
220B ILE* 1.3 62.2 + - - +
221B ILE* 3.7 9.3 + - + +
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B TRP* 3.9 23.8 - - + -
142B GLN 3.2 2.9 - - - -
143B ASN* 4.0 28.5 - - + +
193B ILE* 3.0 27.8 + - + +
194B HIS* 3.1 48.1 + - + +
196B PRO* 4.0 16.6 - - + -
218B TYR* 4.4 4.3 - - + -
219B LEU* 1.3 70.9 - - - +
221B ILE* 1.3 62.7 + - - +
481B PRO* 4.3 12.8 - - + -
485B PRO* 4.2 15.0 - - + -
486B PHE* 6.1 0.4 - - + -
1I NAG 4.3 13.5 - - + +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.1 20.4 - - + -
45B LEU* 3.4 32.5 - - + -
52B LEU* 4.7 6.3 - - + -
141B TRP* 3.2 4.1 - - - -
142B GLN* 2.8 40.4 + - + +
144B CYS* 4.5 8.3 - - + -
190B TRP* 3.9 23.1 - - + -
191B GLU 3.1 8.1 - - - +
192B ILE* 3.7 28.7 - - + -
193B ILE* 4.6 0.7 - - - -
219B LEU* 4.2 16.2 - - + +
220B ILE* 1.3 76.8 - - - +
222B ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE 5.9 2.5 - - - +
140B ASP 4.6 2.2 - - - +
141B TRP* 4.1 15.5 - - + -
190B TRP* 3.4 4.5 - - - -
191B GLU* 2.5 70.5 + - + +
193B ILE* 3.7 23.7 - - + +
221B ILE* 1.3 74.0 - - - +
223B ARG* 1.3 92.0 + - - +
224B LYS* 4.1 17.4 - - - +
225B PRO* 3.7 14.5 - - - +
479B ASN 6.0 0.7 - - - +
480B HIS* 5.2 9.2 - - - +
481B PRO* 4.5 14.6 - - + -
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Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 2.7 37.7 + - - +
132B ILE* 5.4 0.2 - - - +
137B PHE* 3.8 18.8 - - - -
138B PRO* 3.3 25.6 - - - +
139B PHE* 5.6 1.9 - - - -
140B ASP* 2.7 53.6 + - - +
189B GLU* 2.2 50.2 + - + +
190B TRP* 3.4 20.8 - - + -
222B ARG* 1.3 97.3 + - - +
224B LYS* 1.3 69.5 + - - +
225B PRO* 3.2 5.8 - - - +
228B TYR* 4.0 15.2 + - - -
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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