Contacts of the strand formed by residues 180 - 192 (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 ARG 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLN* 3.5 1.0 - - - -
117A LEU* 2.9 29.4 + - + +
177A THR* 3.1 41.3 + - - +
178A GLU 4.7 1.6 - - - +
179A GLY* 1.3 80.2 - - - +
181A LEU* 1.3 66.4 + - - +
211A LEU* 3.6 36.5 + - + +
212A LEU 3.0 32.9 + - - -
213A PRO* 3.5 17.0 + - - +
214A THR 3.4 10.3 - - - -
215A GLU* 4.0 16.6 - - + +
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Residues in contact with LEU 181 (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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95A LEU* 3.7 17.5 - - + -
114A ALA* 5.2 1.3 - - + -
115A GLY 3.6 6.3 - - - +
116A GLN* 4.0 26.0 - - + +
179A GLY 5.1 1.3 - - - +
180A ARG* 1.3 77.3 - - - +
182A LEU* 1.3 61.4 + - - +
211A LEU* 3.9 4.5 - - - +
212A LEU* 3.2 42.7 + - + +
214A THR* 2.9 33.8 + - + +
216A GLN* 4.3 15.5 - - + +
93B LEU* 4.4 9.0 - - + -
94B VAL 4.1 3.8 - - - +
95B LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 182 (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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113A ARG 3.9 0.2 - - - +
114A ALA* 3.5 1.9 - - - -
115A GLY* 2.7 40.3 + - - +
117A LEU* 4.8 12.6 - - + +
144A LEU* 3.9 26.0 - - + -
146A VAL* 4.1 16.4 - - + -
155A CYS* 6.3 0.2 - - + -
157A VAL* 5.8 1.6 - - + -
174A PHE* 4.3 4.5 - - + -
180A ARG 4.7 3.4 - - - +
181A LEU* 1.3 78.2 - - - +
183A LEU* 1.3 60.1 + - - +
184A LEU* 3.8 26.6 + - + +
209A PHE* 3.5 21.3 - - + -
210A SER 3.7 3.4 - - - +
211A LEU* 3.4 33.0 - - + -
212A LEU* 4.9 1.8 - - - -
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Residues in contact with LEU 183 (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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112A PRO* 4.4 4.3 - - + -
113A ARG 3.7 6.7 - - - +
114A ALA* 3.8 30.3 - - + +
182A LEU* 1.3 71.6 - - - +
184A LEU* 1.3 61.7 + - - +
185A GLN* 3.4 25.9 + - + +
209A PHE* 3.1 8.3 - - - +
210A SER* 2.7 41.6 + - - +
212A LEU* 4.1 17.6 - - + +
183B LEU* 3.5 35.2 - - + -
212B LEU* 4.0 29.8 - - + -
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Residues in contact with LEU 184 (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* 3.8 29.4 - - + -
111A SER 4.8 0.7 - - - +
112A PRO* 3.4 1.6 - - - +
113A ARG* 2.8 40.6 + - + +
115A GLY 5.6 0.4 - - - +
146A VAL* 4.8 6.7 - - + -
155A CYS* 4.3 9.9 - - - -
157A VAL* 6.2 0.7 - - + -
182A LEU* 3.8 34.8 - - + +
183A LEU* 1.3 70.5 - - - +
185A GLN* 1.3 63.5 + - - +
186A ASP 3.5 1.6 - - - -
187A CYS* 4.5 17.8 - - - -
204A LEU* 4.0 15.3 - - + -
206A VAL* 4.0 31.6 - - + -
208A ARG 4.0 4.0 - - - -
209A PHE* 4.4 2.0 - - + -
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Residues in contact with GLN 185 (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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111A SER 5.1 2.3 - - - +
112A PRO* 4.1 22.8 - - + +
183A LEU* 3.4 30.9 + - + +
184A LEU* 1.3 72.6 - - - +
186A ASP* 1.3 61.5 + - - +
187A CYS 4.3 0.2 - - - -
208A ARG* 3.0 52.7 + - - +
209A PHE* 3.3 17.7 + - - +
210A SER* 2.9 28.4 + - - -
183B LEU* 4.0 6.7 - - - +
185B GLN* 3.9 17.6 + - - +
208B ARG* 5.5 0.4 - - - +
210B SER* 5.4 2.9 + - - +
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Residues in contact with ASP 186 (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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184A LEU 3.5 0.2 - - - -
185A GLN* 1.3 81.4 - - - +
187A CYS* 1.3 66.4 + - - +
206A VAL* 3.7 0.7 - - - -
207A ASP* 2.8 38.7 + - - +
208A ARG* 3.2 42.3 + - + +
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Residues in contact with CYS 187 (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* 5.7 1.8 - - - -
102A LEU* 4.9 7.9 - - - -
108A THR* 5.2 1.7 - - - +
109A PRO* 3.4 35.0 - - - +
113A ARG* 6.1 3.8 - - - -
184A LEU* 4.5 21.5 - - + -
186A ASP* 1.3 80.0 + - - +
188A GLY* 1.3 61.1 + - - +
204A LEU* 4.9 16.2 - - + -
205A GLN 3.1 17.9 - - - +
206A VAL* 4.0 13.2 - - + -
207A ASP* 4.6 3.6 - - - +
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Residues in contact with GLY 188 (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 LEU* 6.1 0.4 - - - -
108A THR* 5.2 7.2 - - - -
109A PRO* 4.7 7.6 - - - -
187A CYS* 1.3 78.7 - - - +
189A VAL* 1.3 63.2 + - - -
190A HIS* 3.3 16.5 + - - -
204A LEU* 3.5 7.0 - - - -
205A GLN* 3.0 29.0 + - - +
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Residues in contact with VAL 189 (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 LEU* 3.8 29.4 - - + +
103A ILE* 4.1 27.6 - - + +
108A THR* 5.6 3.4 - - - +
109A PRO* 5.4 1.7 - - + +
188A GLY* 1.3 71.1 - - - -
190A HIS* 1.3 67.3 + - - +
202A PHE* 3.7 31.9 - - + -
203A TYR 3.8 6.1 - - - +
204A LEU* 3.7 19.3 - - + -
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Residues in contact with HIS 190 (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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188A GLY* 3.3 32.3 + - - -
189A VAL* 1.3 77.7 + - - +
191A VAL* 1.3 64.5 + - - +
202A PHE* 3.4 7.0 - - - -
203A TYR* 2.9 59.3 + - + +
205A GLN* 3.5 38.9 + - + +
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Residues in contact with VAL 191 (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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190A HIS* 1.3 75.1 - - - +
192A GLN* 1.3 67.8 + - - +
193A VAL* 3.9 7.1 + - + +
201A GLU 3.7 2.9 - - - -
202A PHE* 3.7 27.6 - - + -
203A TYR* 4.0 5.2 - - - -
234A LEU* 3.9 20.6 - - + -
237A CYS* 4.0 20.0 - - + -
238A LEU* 4.1 21.3 - - + +
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Residues in contact with GLN 192 (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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154A ARG* 3.9 27.1 + - - +
191A VAL* 1.3 73.7 - - - +
193A VAL* 1.3 89.7 + - - +
195A GLU* 3.7 25.3 + - + +
200A ALA* 3.1 5.6 - - - +
201A GLU* 2.8 48.1 + - + +
203A TYR* 3.7 23.9 + - + -
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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