Contacts of the strand formed by residues 182 - 190 (chain A) in PDB entry 5I2S
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 ILE 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.2 3.9 - - - -
45A MET 2.9 31.4 + - - +
47A LYS* 4.0 38.1 - - + +
48A SER* 5.6 0.7 - - - -
179A SER* 4.7 4.9 - - - +
180A ASN* 3.2 22.0 - - + +
181A LEU* 1.3 73.7 - - - +
183A SER* 1.3 76.9 + - - +
184A MET* 3.5 16.8 - - + +
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Residues in contact with SER 183 (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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42A GLN* 6.6 0.2 - - - -
43A VAL 3.3 7.6 - - - -
44A LYS* 3.8 26.4 + - - +
181A LEU 4.1 1.8 + - - -
182A ILE* 1.3 86.6 - - - +
184A MET* 1.3 65.0 + - - +
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Residues in contact with MET 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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42A GLN* 3.7 2.3 - - - +
43A VAL* 2.9 45.7 + - + +
45A MET* 4.1 33.0 - - + +
47A LYS* 3.5 40.4 - - + -
50A LYS* 5.5 1.8 - - - +
182A ILE* 3.5 23.3 - - + +
183A SER* 1.3 77.6 - - - +
185A ASP* 1.3 68.1 + - - +
186A ILE* 4.8 3.6 - - + -
209A TYR* 4.9 16.2 - - + -
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Residues in contact with ASP 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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40A ALA* 4.4 21.4 - - + +
41A LEU 3.4 4.6 + - - +
42A GLN* 3.3 33.6 + - - +
184A MET* 1.3 80.4 - - - +
186A ILE* 1.3 66.1 + - - +
207A SER* 4.9 2.8 - - - -
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Residues in contact with ILE 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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40A ALA* 3.6 3.5 - - - -
41A LEU* 2.8 45.9 + - + +
43A VAL* 3.6 23.3 - - + -
45A MET* 4.4 7.4 - - - -
184A MET* 4.1 4.2 + - + -
185A ASP* 1.3 79.0 - - - +
187A THR* 1.3 62.1 + - - +
205A PHE* 3.9 17.0 - - + -
206A ARG 3.7 8.3 - - - +
207A SER* 3.5 23.3 - - - +
210A PHE* 4.2 13.9 - - + -
237A PHE* 3.8 41.3 - - + -
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Residues in contact with THR 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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38A GLY* 3.8 15.9 - - - -
39A THR 3.3 13.0 - - - +
40A ALA* 4.8 0.2 - - - +
186A ILE* 1.3 75.9 - - - +
188A PHE* 1.3 60.8 + - - +
189A PHE* 3.6 32.0 - - + -
205A PHE* 3.4 7.4 - - - +
206A ARG* 2.8 47.6 + - - +
207A SER* 5.1 2.1 - - - -
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Residues in contact with PHE 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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37A ILE 3.5 2.1 - - - +
38A GLY* 3.5 0.7 - - - -
39A THR* 2.9 36.4 + - - +
41A LEU* 4.4 11.4 - - + -
186A ILE 3.9 1.2 + - - -
187A THR* 1.3 71.2 - - - +
189A PHE* 1.3 67.6 + - - +
190A SER* 3.7 22.1 + - - -
194A GLU 3.7 13.5 - - - -
195A LEU* 3.7 27.8 - - + -
197A SER 3.4 24.7 - - - -
198A LEU* 3.7 19.3 - - + -
199A GLY 4.8 0.4 - - - -
203A THR* 3.6 22.9 - - + -
204A GLY 3.3 12.1 - - - -
205A PHE* 3.4 33.0 - + + -
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Residues in contact with PHE 189 (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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33A HIS* 3.7 35.7 - + + -
36A LEU* 3.6 26.2 - - + -
37A ILE 3.2 6.5 - - - -
38A GLY* 3.8 22.7 - - - -
187A THR* 3.6 26.5 - - + -
188A PHE* 1.3 73.2 - - - +
190A SER* 1.3 59.9 + - - +
203A THR* 3.3 9.5 - - - +
204A GLY* 2.8 42.6 + - - +
206A ARG* 3.6 44.6 - - + -
212A TYR* 3.7 16.4 - + + -
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Residues in contact with SER 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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36A LEU* 3.5 9.2 - - - +
37A ILE* 2.8 30.2 + - - +
39A THR* 5.0 0.2 + - - -
188A PHE* 3.7 24.0 + - - -
189A PHE* 1.3 75.9 - - - +
191A GLU* 1.3 63.9 + - - +
192A ASP* 3.8 13.7 - - - -
193A GLY* 3.2 6.8 - - - -
194A GLU 3.2 21.9 + - - -
197A SER* 3.9 9.9 - - - -
203A THR* 4.1 7.0 - - - -
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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