Contacts of the strand formed by residues 201 - 215 (chain A) in PDB entry 5I2Y
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 2.8 48.0 + - - +
191A VAL* 3.7 2.1 - - - +
192A GLN* 2.8 40.9 + - + +
198A ALA* 5.7 3.6 - - - +
199A PRO 4.3 7.3 - - - +
200A ALA* 1.3 78.3 - - - +
202A PHE* 1.3 68.7 + - - +
225A ASN* 3.6 23.4 + - + +
234A LEU* 3.8 11.0 - - - +
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Residues in contact with PHE 202 (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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103A ILE* 3.6 35.4 - - + -
153A VAL* 4.4 6.3 - - - +
154A ARG 5.2 0.5 + - - -
189A VAL* 3.7 25.4 - - + -
190A HIS 3.4 7.6 - - - -
191A VAL* 3.7 22.4 - - + -
201A GLU* 1.3 81.1 - - - +
203A TYR* 1.3 61.9 + - - +
225A ASN* 3.1 28.4 + - - +
230A VAL* 3.5 28.5 - - + -
233A LYS* 3.9 10.3 - - + -
234A LEU* 3.4 42.8 - - + -
237A CYS* 3.8 17.3 - - - -
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Residues in contact with TYR 203 (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 VAL* 4.2 4.9 - - - -
154A ARG* 3.4 45.8 - - + +
156A LEU* 4.1 28.0 - - + +
189A VAL* 3.8 2.5 - - - +
190A HIS* 2.9 66.2 + - + +
191A VAL 4.0 2.7 - - - -
192A GLN* 3.7 40.8 + - + -
201A GLU* 4.3 1.3 - - - +
202A PHE* 1.3 76.0 - - - +
204A LEU* 1.3 82.7 + - - +
205A GLN* 4.4 11.7 + - + -
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Residues in contact with LEU 204 (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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98A TRP* 3.7 33.4 - - + -
99A ILE* 5.4 1.8 - - + -
102A LEU* 4.4 9.6 - - + -
103A ILE* 5.4 4.9 - - + -
153A VAL* 3.8 27.6 - - + -
154A ARG 3.0 7.1 + - - -
155A CYS* 3.3 19.2 - - + -
156A LEU 2.8 26.0 + - - -
184A LEU* 4.0 7.6 - - + -
187A CYS* 4.9 8.3 - - + -
188A GLY 3.5 9.2 - - - +
189A VAL* 3.7 30.3 - - + -
203A TYR* 1.3 82.1 - - - +
205A GLN* 1.3 62.3 + - - +
206A VAL* 4.0 2.7 - - + -
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Residues in contact with GLN 205 (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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156A LEU* 3.5 17.1 - - + +
158A THR* 3.4 24.7 + - - +
187A CYS* 3.1 23.8 - - - +
188A GLY 3.0 9.8 + - - -
190A HIS* 3.5 38.2 + - + +
203A TYR* 4.1 13.2 + - + -
204A LEU* 1.3 73.0 - - - +
206A VAL* 1.3 61.3 + - - +
207A ASP* 3.3 25.6 + - - +
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Residues in contact with VAL 206 (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 CYS* 4.1 25.4 - - + -
156A LEU 2.8 13.2 + - - +
157A VAL* 4.2 11.7 - - + -
158A THR* 2.9 29.0 + - - -
161A ALA* 3.7 2.6 - - - +
184A LEU* 4.0 31.0 - - + -
186A ASP 3.7 4.9 - - - +
187A CYS* 4.3 4.9 - - + -
204A LEU* 4.7 1.6 - - + -
205A GLN* 1.3 77.0 - - - +
207A ASP* 1.3 58.3 + - - +
208A ARG 3.5 25.6 - - - +
209A PHE* 3.9 22.7 - - + -
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Residues in contact with ASP 207 (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 THR* 3.2 26.9 + - - +
160A GLU* 3.3 33.4 - - - +
161A ALA* 3.3 20.7 - - - +
164A THR* 4.9 1.0 + - - -
186A ASP* 2.8 24.6 + - + +
187A CYS* 5.4 2.1 - - - -
205A GLN* 3.3 25.6 + - - +
206A VAL* 1.3 72.6 - - - +
208A ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 208 (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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161A ALA* 3.7 6.0 - - - +
164A THR* 5.0 9.6 - - - +
185A GLN* 3.0 71.4 + - - +
186A ASP* 3.2 36.2 + - + +
206A VAL* 3.5 7.6 - - - +
207A ASP* 1.3 81.0 - - - +
209A PHE* 1.3 67.5 + - - +
185B GLN* 5.2 3.6 + - - +
208B ARG* 5.2 7.6 - - - +
210B SER* 5.8 2.4 + - - -
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Residues in contact with PHE 209 (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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157A VAL* 3.8 28.7 - - + -
161A ALA* 3.8 18.4 - - + -
162A LEU* 4.2 3.4 - - + -
165A SER* 3.6 34.6 + - - -
167A TRP* 3.9 18.6 - + - -
174A PHE* 3.4 20.0 - + - -
182A LEU* 3.5 17.9 - - + -
183A LEU 3.1 15.0 - - - +
184A LEU* 4.4 5.4 - - + -
185A GLN* 3.3 11.7 + - - +
206A VAL* 3.9 11.4 - - + -
208A ARG* 1.3 78.6 - - - +
210A SER* 1.3 66.1 + - - +
211A LEU* 3.5 26.0 - - + -
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Residues in contact with SER 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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182A LEU* 3.7 2.1 - - - +
183A LEU* 2.7 44.2 + - - +
185A GLN* 2.9 27.9 + - - -
209A PHE* 1.3 80.4 + - - +
211A LEU* 1.3 60.8 + - - +
212A LEU* 4.8 0.2 - - - -
112B PRO* 4.1 25.2 - - - +
185B GLN* 5.3 1.4 + - - +
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Residues in contact with LEU 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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117A LEU* 5.9 1.6 - - + -
167A TRP* 5.2 9.6 - - + -
174A PHE* 3.8 12.1 - - + -
177A THR* 3.9 26.0 - - + +
180A ARG* 3.6 43.0 + - + +
181A LEU 3.9 7.2 - - - +
182A LEU* 3.4 26.0 - - + -
209A PHE* 3.5 17.6 - - + -
210A SER* 1.3 74.1 - - - +
212A LEU* 1.3 61.8 + - - +
213A PRO* 4.6 0.2 - - - +
111B SER* 4.9 2.9 - - - -
112B PRO* 3.5 22.3 - - - +
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Residues in contact with LEU 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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114A ALA* 4.9 7.9 - - + -
180A ARG* 3.0 24.1 + - - -
181A LEU* 3.2 43.2 + - + +
183A LEU* 4.1 33.4 - - + +
210A SER* 3.7 1.3 + - - +
211A LEU* 1.3 81.3 - - - +
213A PRO* 1.3 71.2 - - + +
214A THR* 3.3 5.8 + - - +
95B LEU* 4.8 3.6 - - + -
111B SER* 6.1 0.2 - - - -
112B PRO* 3.9 13.9 - - + +
114B ALA* 4.3 23.6 - - + +
183B LEU* 3.9 24.5 - - + -
212B LEU* 5.7 0.9 - - + -
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Residues in contact with PRO 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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180A ARG* 3.5 20.3 + - - +
211A LEU 4.6 0.4 - - - +
212A LEU* 1.3 87.4 - - + +
214A THR* 1.3 68.7 + - - +
215A GLU* 3.3 3.8 + - - +
98B TRP* 5.3 7.0 - - + -
111B SER* 5.3 6.4 - - - +
112B PRO* 3.3 20.2 - - + +
113B ARG* 3.9 40.2 - - - +
114B ALA 5.8 0.2 - - - +
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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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180A ARG* 3.4 3.8 - - - -
181A LEU* 2.9 52.0 + - + -
212A LEU* 3.3 3.7 - - - +
213A PRO* 1.3 84.3 - - - +
215A GLU* 1.3 71.0 + - - +
216A GLN* 4.8 1.3 - - + -
94B VAL 3.6 17.9 - - - +
95B LEU* 4.0 11.1 - - - +
96B ARG* 3.3 42.8 + - + +
98B TRP* 5.7 1.6 - - - -
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Residues in contact with GLU 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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176A GLY 5.5 2.0 - - - +
178A GLU 3.6 17.1 - - - +
179A GLY* 3.6 13.6 - - - +
180A ARG* 4.0 16.8 - - - +
213A PRO 3.3 3.6 + - - +
214A THR* 1.3 74.6 - - - +
216A GLN* 1.3 71.9 + - - +
96B ARG* 3.1 29.5 + - - +
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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