Contacts of the strand formed by residues 209 - 218 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLN* 4.0 12.1 - - - -
156A LEU 3.2 9.6 - - - -
157A GLU* 3.8 23.6 - - + -
168A PHE* 5.2 0.4 - - - -
197A TYR* 3.6 7.8 - - - +
198A CYS* 2.1 79.2 + - - +
199A THR* 3.7 5.8 + - - +
200A LYS* 3.9 8.5 - - + -
207A PHE 3.6 4.8 + - - +
208A THR* 1.3 80.3 + - - +
210A ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 210 (chain A).
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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41A CYS* 4.2 12.3 - - + -
154A MET 3.9 0.3 - - - +
155A GLN* 3.5 2.3 - - - -
156A LEU* 2.7 50.9 + - + +
168A PHE* 3.6 32.1 - - + +
169A GLU* 3.9 13.0 - - - +
170A TRP* 3.6 54.3 - - + +
196A ARG 3.5 6.1 - - - +
197A TYR* 4.0 20.2 - - + -
198A CYS* 3.5 1.6 - - - -
208A THR* 5.1 0.2 - - - +
209A CYS* 1.3 79.3 - - - +
211A GLU* 1.3 60.3 + - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 4.1 14.1 - - + +
154A MET 3.3 10.1 - - - +
155A GLN* 3.0 30.1 + - + -
170A TRP* 3.1 17.0 + - - -
194A ASP 4.5 0.2 - - - -
195A LEU* 3.5 1.9 - - - -
196A ARG* 2.9 43.3 + - + +
197A TYR 5.0 0.6 - - - +
198A CYS* 3.5 15.6 - - + +
210A ILE* 1.3 76.6 - - - +
212A VAL* 1.3 68.8 + - - +
213A ARG* 2.8 42.8 + - + -
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Residues in contact with VAL 212 (chain A).
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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43A ILE* 4.6 3.8 - - + -
152A CYS 4.0 0.5 - - - +
153A ILE* 3.3 4.0 - - - +
154A MET* 3.0 54.4 + - + +
170A TRP* 3.7 24.0 - - + -
176A VAL* 4.0 11.0 - - + -
193A LYS* 4.0 18.4 - - + -
194A ASP 3.4 8.7 - - - +
195A LEU* 4.0 13.2 - - + -
211A GLU* 1.3 74.8 - - - +
213A ARG* 1.3 65.1 + - - +
214A PHE* 3.9 24.5 - - + -
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A THR* 3.8 30.6 - - + +
152A CYS 3.6 3.6 - - - -
153A ILE* 3.9 17.6 - - + +
193A LYS* 3.4 10.6 - - - +
194A ASP* 2.8 55.6 + - - +
196A ARG* 3.4 39.5 - - - +
211A GLU* 2.8 32.8 + - + +
212A VAL* 1.3 77.1 - - - +
214A PHE* 1.3 63.6 + - - +
215A HIS* 4.2 2.8 + - - +
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.5 1.8 - - + -
45A ILE* 3.5 33.7 - - + -
48A PHE* 4.0 23.8 - + + -
58A TYR* 4.0 18.8 - - - -
150A GLN 3.7 0.5 - - - +
151A THR* 3.3 6.8 - - - +
152A CYS* 2.8 45.3 + - + +
154A MET* 4.1 16.4 - - + -
176A VAL* 4.3 3.1 - - + -
189A LEU* 3.9 18.8 - - + -
193A LYS* 3.7 33.4 - - + -
212A VAL* 3.9 31.4 - - + -
213A ARG* 1.3 73.7 - - - +
215A HIS* 1.3 62.3 + - - +
216A LEU* 4.0 3.1 + - + +
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Residues in contact with HIS 215 (chain A).
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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149A VAL* 4.8 9.4 - - + +
150A GLN 3.6 3.7 + - - +
151A THR* 3.3 32.7 + - + +
188A LEU 3.5 0.3 - - - +
189A LEU* 3.7 6.1 - - - +
190A LYS* 3.0 49.6 + - + +
192A GLU* 3.6 29.3 + - - -
194A ASP* 2.8 34.8 + - - -
213A ARG 4.4 4.8 + - - -
214A PHE* 1.3 74.1 - - - +
216A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 216 (chain A).
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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48A PHE* 4.2 14.1 - - + -
51A ILE* 3.9 22.7 - - + -
149A VAL* 3.3 5.6 - - - +
150A GLN* 2.9 43.6 + - + +
152A CYS* 3.7 32.5 - - + -
184A LEU* 3.8 27.8 - - + -
187A PHE* 3.7 20.9 - - + -
188A LEU 3.4 1.3 - - - -
189A LEU* 4.0 28.3 - - + -
214A PHE 4.8 2.9 - - - +
215A HIS* 1.3 74.3 - - - +
217A GLU* 1.3 61.4 + - - +
218A ARG 3.9 1.2 + - - -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASP 4.3 4.0 - - - +
149A VAL* 4.3 11.2 - - + -
187A PHE* 3.3 3.8 - - - -
188A LEU* 2.8 52.8 + - + +
190A LYS* 4.7 14.8 - - + +
215A HIS 4.1 0.8 - - - -
216A LEU* 1.3 71.9 - - - +
218A ARG* 1.3 65.4 + - - +
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.0 39.6 + - - +
140A MET* 4.8 0.6 - - - -
142A LEU* 4.2 3.8 - - - +
145A PHE* 3.5 15.3 - - - -
146A PRO* 3.4 21.5 - - - +
147A MET* 5.5 2.3 - - - -
148A ASP* 2.6 59.8 + - - +
150A GLN* 4.8 3.6 - - - +
186A GLN* 3.6 21.0 + - + +
187A PHE* 3.5 27.3 - - + -
216A LEU 3.9 0.2 + - - -
217A GLU* 1.3 73.7 - - - +
219A GLN* 1.3 69.8 + - - +
220A MET* 3.8 2.4 + - - +
223A TYR* 3.6 32.2 + - + -
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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