Contacts of the strand formed by residues 209 - 220 (chain A) in PDB entry 6I53
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 GLU 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A THR* 3.3 8.6 - - - -
164A ARG* 2.6 73.8 + - + +
202A ILE* 4.1 11.2 - - + -
203A VAL 3.5 11.2 - - - +
204A GLN* 3.3 26.6 - - - +
208A GLY* 1.3 72.3 - - - -
210A TYR* 1.3 55.2 + - - +
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Residues in contact with TYR 210 (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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102A HIS* 5.5 3.8 - + + +
159A SER* 3.8 17.9 - - - +
160A TYR 3.5 24.3 + - - -
161A ALA 3.9 1.1 - - - -
162A TYR 3.2 34.8 - - - +
163A THR* 3.7 13.0 - - + -
164A ARG* 4.2 3.1 - - - +
202A ILE* 3.4 10.7 - - - +
203A VAL* 3.3 44.5 + - + -
205A SER* 4.0 10.3 - - - -
207A THR* 2.4 32.4 + - - -
208A GLY 3.3 24.7 - - - -
209A GLU* 1.3 73.0 - - - +
211A VAL* 1.3 67.2 + - - +
212A VAL* 3.7 4.5 + - + +
115E MET* 4.3 3.1 - - - +
117E ARG* 3.2 15.1 + - - -
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Residues in contact with VAL 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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158A GLY* 3.7 18.9 - - - -
159A SER* 4.2 3.0 + - - -
162A TYR 5.7 0.2 + - - -
163A THR 5.2 0.2 - - - -
164A ARG* 3.7 31.9 - - + +
167A VAL 4.2 16.4 + - - +
168A VAL* 4.2 14.4 - - + -
169A TYR* 3.7 42.7 - - + +
200A SER* 5.8 0.4 - - - -
201A GLY 3.8 6.7 - - - +
202A ILE* 5.0 4.3 - - + +
210A TYR* 1.3 72.9 - - - +
212A VAL* 1.3 62.4 + - - +
213A MET* 3.7 14.6 - - + -
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Residues in contact with VAL 212 (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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102A HIS* 3.4 39.0 - - + +
156A LYS* 4.3 6.1 - - + -
157A PHE 3.6 2.7 - - - +
200A SER* 3.4 2.3 - - - -
201A GLY 2.6 48.8 + - - +
203A VAL* 3.7 27.8 - - + +
210A TYR* 3.9 9.4 - - + +
211A VAL* 1.3 76.9 - - - +
213A MET* 1.3 76.5 + - - +
214A THR* 4.0 7.8 + - - +
56G ILE* 4.4 14.6 - - + -
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Residues in contact with MET 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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43A THR* 4.3 2.2 - - - +
155A LEU 4.7 0.7 - - - -
156A LYS* 3.3 3.9 - - - -
157A PHE* 2.9 67.5 + - + +
169A TYR* 3.3 40.6 - - + +
170A GLU* 4.3 2.9 - - - -
171A TRP* 3.1 45.8 - - + -
199A ASP 4.1 1.6 - - - -
200A SER* 3.7 22.4 - - - -
211A VAL* 3.7 19.7 + - + -
212A VAL* 1.3 73.6 - - - +
214A THR* 1.3 68.0 + - - +
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Residues in contact with THR 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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155A LEU 3.8 4.5 - - - -
156A LYS* 3.7 15.9 - - + +
171A TRP* 4.3 0.8 - - - -
198A VAL* 3.5 3.1 - - - +
199A ASP* 2.8 43.3 + - + +
212A VAL* 4.0 7.8 + - - +
213A MET* 1.3 80.0 + - - +
215A THR* 1.3 66.8 + - - +
216A HIS* 3.4 31.0 - - + +
58G TYR* 2.9 41.0 + - + +
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Residues in contact with THR 215 (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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45A ILE* 4.6 2.9 - - - +
154A PRO 3.5 0.9 - - - -
155A LEU* 2.8 46.1 + - - +
157A PHE* 5.2 0.2 - - - -
171A TRP* 3.7 11.3 - - - -
179A VAL* 3.5 34.5 - - + +
196A GLN* 4.2 11.7 - - + -
197A THR 3.4 8.1 - - - +
198A VAL* 4.1 3.9 - - + +
214A THR* 1.3 75.4 + - - +
216A HIS* 1.3 62.8 + - - +
217A PHE* 3.6 32.9 + - + -
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Residues in contact with HIS 216 (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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152A ALA* 3.9 17.4 + - + +
153A CYS 3.7 2.5 - - - +
154A PRO* 3.5 30.5 - - + +
196A GLN* 3.3 2.8 - - - -
197A THR* 2.7 48.3 + - + +
199A ASP* 5.4 2.0 - - + -
214A THR* 3.4 27.1 - - + +
215A THR* 1.3 70.0 - - - +
217A PHE* 1.3 62.9 + - - +
218A HIS* 3.6 21.7 + + + +
33G ILE* 4.9 10.5 - - + -
52G ASP* 4.2 14.3 + - - -
58G TYR* 4.1 2.0 + - - -
100G GLY 5.6 2.0 - - - -
103G GLY 5.6 0.7 - - - -
104G LEU* 3.4 33.0 - - + +
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Residues in contact with PHE 217 (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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47A VAL* 3.8 19.7 - - + -
50A PHE* 3.5 36.8 - + + -
60A TYR* 4.4 5.4 - - - -
62A ILE* 3.6 27.8 - - + -
151A HIS 3.7 0.5 - - - +
152A ALA* 3.4 0.3 - - - -
153A CYS* 2.8 47.1 + - - +
155A LEU* 4.1 12.8 - - + -
179A VAL* 4.1 4.5 - - + -
181A VAL* 4.3 12.6 - - + -
193A LEU* 4.1 17.9 - - + -
195A GLY 4.2 1.6 - - - -
196A GLN* 3.8 21.5 - - + -
215A THR* 3.7 31.2 - - + -
216A HIS* 1.3 71.9 - - - +
218A HIS* 1.3 61.0 + - - +
219A LEU* 3.8 1.4 + - - +
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Residues in contact with HIS 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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151A HIS 3.4 2.9 - - - -
152A ALA* 3.4 19.1 - - + +
193A LEU* 3.4 6.8 - - - +
194A LEU* 3.0 27.8 + - + -
195A GLY 3.1 29.7 + - - +
196A GLN 4.1 0.2 - - - -
197A THR* 2.7 33.4 + - - -
216A HIS* 3.6 17.4 + - + -
217A PHE* 1.3 70.3 - - - +
219A LEU* 1.3 61.0 + - - +
100G GLY 3.5 13.9 - - - -
101G PHE* 3.6 17.5 - - + -
102G TRP* 3.2 48.3 + + + -
103G GLY 4.0 2.7 - - - -
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Residues in contact with LEU 219 (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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50A PHE* 3.7 26.0 - - + -
53A VAL* 3.8 28.9 - - + -
150A ALA* 3.4 1.9 - - - +
151A HIS* 2.7 27.2 + - + +
153A CYS* 3.8 24.5 - - - -
188A LEU* 3.8 19.5 - - + -
191A TYR* 4.0 21.3 - - + -
192A ASP 3.5 4.7 - - - +
193A LEU* 3.9 17.3 - - + -
194A LEU* 4.8 0.7 - - - -
217A PHE 4.4 5.6 - - - +
218A HIS* 1.3 73.7 - - - +
220A LYS* 1.3 63.0 + - - +
101G PHE* 3.2 20.1 - - - -
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Residues in contact with LYS 220 (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 MET* 5.1 5.8 - - - +
149A ASP 3.4 25.4 - - - +
150A ALA* 3.8 13.9 - - + +
191A TYR* 4.0 1.5 - - - -
192A ASP* 3.0 37.4 + - + +
194A LEU* 3.8 27.1 - - + +
219A LEU* 1.3 78.3 - - - +
221A ARG* 1.3 69.5 + - - +
222A LYS* 3.3 2.1 + - - +
418A ARG 5.2 9.4 + - - -
101G PHE* 4.9 1.8 - - + -
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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