Contacts of the strand formed by residues 209 - 218 (chain B) in PDB entry 5TIN
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 CYS 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B GLN* 4.0 11.7 - - - -
156B LEU 3.2 10.5 - - - -
157B GLU* 3.8 23.8 - - + -
168B PHE* 5.2 0.2 - - - -
197B TYR* 3.6 6.4 - - - +
198B CYS* 2.1 79.2 + - - +
199B THR* 3.7 6.9 + - - +
200B LYS* 3.9 7.6 - - + -
207B PHE 3.6 4.6 + - - +
208B THR* 1.3 79.9 + - - +
210B ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 210 (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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41B CYS* 4.2 11.9 - - + -
154B MET 3.9 0.2 - - - +
155B GLN* 3.4 2.3 - - - -
156B LEU* 2.7 50.2 + - + +
168B PHE* 3.6 31.4 - - + +
169B GLU* 3.8 12.1 - - - +
170B TRP* 3.6 54.1 - - + +
196B ARG 3.5 4.7 - - - +
197B TYR* 4.0 19.5 - - + -
198B CYS* 3.5 1.0 - - - -
208B THR* 5.1 0.2 - - - +
209B CYS* 1.3 80.4 - - - +
211B GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 211 (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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153B ILE* 4.1 13.6 - - + +
154B MET 3.3 10.1 - - - +
155B GLN* 3.0 30.3 + - + -
170B TRP* 3.1 14.1 + - - -
194B ASP 3.9 0.4 - - - +
195B LEU* 3.5 0.9 - - - -
196B ARG* 2.9 46.7 + - + +
197B TYR 5.0 1.2 - - - +
198B CYS* 3.5 16.0 - - - +
210B ILE* 1.3 77.0 - - - +
212B VAL* 1.3 70.7 + - - +
213B ARG* 2.8 42.7 + - + +
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Residues in contact with VAL 212 (chain B).
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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43B ILE* 4.5 4.0 - - + -
152B CYS 4.0 0.2 - - - +
153B ILE* 3.3 4.2 - - - +
154B MET* 3.0 55.0 + - + +
170B TRP* 3.7 24.2 - - + -
176B VAL* 4.0 10.5 - - + -
193B LYS* 4.0 19.1 - - + -
194B ASP 3.4 8.3 - - - +
195B LEU* 4.0 13.0 - - + -
211B GLU* 1.3 75.7 - - - +
213B ARG* 1.3 64.7 + - - +
214B PHE* 3.9 24.2 - - + -
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Residues in contact with ARG 213 (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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151B THR* 3.8 29.8 - - + +
152B CYS 3.6 3.8 - - - -
153B ILE* 3.9 17.6 - - + +
193B LYS* 3.4 10.9 - - - +
194B ASP* 2.8 59.7 + - - +
196B ARG* 4.1 17.1 - - + +
211B GLU* 2.8 32.9 + - + +
212B VAL* 1.3 76.1 - - - +
214B PHE* 1.3 62.5 + - - +
215B HIS* 4.2 2.8 + - - +
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Residues in contact with PHE 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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43B ILE* 4.5 2.0 - - + -
45B ILE* 3.5 34.3 - - + -
48B PHE* 4.0 22.4 - + + -
58B TYR* 4.0 17.9 - + - -
150B GLN 3.7 0.5 - - - +
151B THR* 3.3 6.6 - - - +
152B CYS* 2.8 45.8 + - + +
154B MET* 4.1 16.2 - - + -
176B VAL* 4.3 3.4 - - + -
189B LEU* 3.9 19.7 - - + -
193B LYS* 3.7 33.4 - - + -
212B VAL* 3.9 32.5 - - + -
213B ARG* 1.3 74.5 - - - +
215B HIS* 1.3 62.9 + - - +
216B LEU* 4.0 2.5 + - + +
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Residues in contact with HIS 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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149B VAL* 4.8 10.3 - - + +
150B GLN 3.6 3.1 + - - +
151B THR* 3.3 32.9 + - + -
188B LEU 3.5 0.3 - - - +
189B LEU* 3.7 5.7 - - - +
190B LYS* 3.0 49.3 + - + +
192B GLU* 3.6 28.9 + - - -
194B ASP* 2.8 35.2 + - - -
213B ARG 4.3 5.0 + - - -
214B PHE* 1.3 74.4 + - - +
216B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 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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48B PHE* 4.2 13.0 - - + -
51B ILE* 3.9 22.0 - - + -
149B VAL* 3.3 5.7 - - - +
150B GLN* 2.9 44.6 + - + +
152B CYS* 3.7 32.8 - - + -
184B LEU* 3.8 27.8 - - + -
187B PHE* 3.7 23.2 - - + -
188B LEU 3.4 1.1 - - - -
189B LEU* 4.0 26.9 - - + -
214B PHE 4.8 3.1 - - - +
215B HIS* 1.3 74.5 - - - +
217B GLU* 1.3 60.9 + - - +
218B ARG 3.9 0.7 + - - -
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Residues in contact with GLU 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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148B ASP 4.3 3.1 - - - +
149B VAL* 4.3 14.6 - - + -
187B PHE* 3.3 3.1 - - - -
188B LEU* 2.8 58.3 + - + +
190B LYS* 3.7 30.9 + - + +
215B HIS 4.1 0.8 - - - -
216B LEU* 1.3 72.0 - - - +
218B ARG* 1.3 71.6 + - - +
219B GLN 3.5 0.2 + - - -
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Residues in contact with ARG 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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53B GLU* 3.0 39.0 + - - +
140B MET* 4.8 0.6 - - - -
142B LEU* 4.2 3.6 - - - +
145B PHE* 3.5 15.6 - - - -
146B PRO* 3.4 22.0 - - - +
147B MET* 5.5 2.6 - - - -
148B ASP* 2.6 59.9 + - - +
150B GLN* 4.8 4.2 - - - +
186B GLN* 3.6 21.8 + - + +
187B PHE* 3.5 27.7 - - + -
216B LEU 3.9 0.2 + - - -
217B GLU* 1.3 79.2 - - - +
219B GLN* 1.3 71.2 + - - +
220B MET* 3.8 2.6 + - - +
223B TYR* 3.6 32.8 + - + -
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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