Contacts of the strand formed by residues 186 - 193 (chain A) in PDB entry 1S0R
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 LYS 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 4.4 0.4 - - - -
104A SER* 3.5 21.9 + - - +
105A LEU 3.7 18.6 + - - +
106A PRO* 4.1 17.9 - - + -
107A THR* 5.1 16.4 - - - +
182A VAL* 3.2 5.6 - - - +
183A CYS 2.9 31.7 + - - +
184A SER* 3.8 12.8 - - - +
185A GLY* 1.3 85.8 + - - +
187A LEU* 1.3 59.4 + - - +
188A GLN* 3.1 19.9 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.6 35.9 - - - +
30A ILE* 4.2 17.9 - - + -
36A VAL* 4.3 18.6 - - + -
103A ILE* 4.0 11.7 - - + +
104A SER 2.9 18.1 + - - +
105A LEU* 4.6 8.3 - - + -
106A PRO* 3.1 23.7 - - + +
180A PRO* 3.7 15.5 - - + -
181A VAL 3.8 4.9 - - - +
182A VAL* 4.0 6.5 - - + -
186A LYS* 1.3 68.9 - - - +
188A GLN* 1.3 57.5 + - - +
189A GLY 3.5 23.6 - - - +
190A ILE* 5.2 1.6 - - + -
209A VAL* 3.3 15.8 - - + +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 3.5 24.9 - - - +
108A SER 3.0 23.1 + - - +
109A CYS* 3.9 3.8 - - - -
110A ALA* 3.7 34.7 + - + +
142A ILE* 5.1 0.2 - - + -
161A PHE* 3.3 17.8 - - + -
181A VAL 2.9 5.7 + - - -
183A CYS* 3.8 30.8 + - + +
186A LYS* 3.1 21.5 + - + +
187A LEU* 1.3 72.8 - - - +
189A GLY* 1.3 58.4 + - - +
208A LYS* 3.9 1.0 - - - +
209A VAL* 3.0 24.5 + - - -
210A CYS* 4.0 6.1 - - - +
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Residues in contact with GLY 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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161A PHE* 3.7 9.4 - - - -
180A PRO* 3.8 0.9 - - - +
181A VAL* 2.9 40.9 + - - +
187A LEU* 3.5 14.3 - - - +
188A GLN* 1.3 79.6 - - - +
190A ILE* 1.3 63.8 + - - +
206A TYR* 4.5 0.4 - - - -
207A THR 3.2 9.4 - - - -
209A VAL* 3.8 1.6 - - - -
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Residues in contact with ILE 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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28A SER* 6.2 0.2 - - - +
36A VAL* 3.4 31.6 - - + -
37A SER 3.6 3.1 - - - +
38A ALA* 3.8 14.8 - - + +
84A ASP 4.2 2.0 - - - +
85A ILE* 3.6 30.5 - - + -
178A GLY* 3.6 31.2 - - - +
179A GLY 3.3 4.7 - - - +
181A VAL* 4.3 0.2 - - - +
187A LEU* 5.2 2.5 - - + -
189A GLY* 1.3 78.7 - - - +
191A VAL* 1.3 71.7 + - - +
192A SER* 3.1 2.1 + - - -
206A TYR* 3.2 7.2 - - - -
207A THR* 2.9 38.8 + - - +
209A VAL* 3.7 14.4 - - + -
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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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38A ALA* 4.0 4.0 - - - +
40A HIS* 4.0 0.3 - - - -
118A ILE* 4.1 18.4 - - + -
119A SER 4.9 1.6 - - - +
172A SER* 3.6 21.5 - - - +
176A ASP* 3.4 26.2 - - + +
177A SER* 3.6 21.7 - - - +
178A GLY 2.9 23.9 + - - +
179A GLY* 2.9 22.4 + - - +
180A PRO 4.6 0.9 - - - +
181A VAL* 4.7 0.2 - - - +
190A ILE* 1.3 73.9 - - - +
192A SER* 1.3 60.2 + - - +
206A TYR* 3.6 21.0 - - + -
225A BEN 3.7 15.5 - - + -
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Residues in contact with SER 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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40A HIS* 3.0 23.4 + - - -
81A LEU* 4.2 2.9 + - - +
84A ASP* 2.7 33.1 + - - +
160A MET* 5.9 1.5 - - - +
190A ILE 3.1 3.6 + - - -
191A VAL* 1.3 75.3 - - - +
193A TRP* 1.3 82.0 + - - +
205A VAL 3.2 14.3 + - - -
206A TYR* 4.1 0.9 - - - -
207A THR* 3.7 21.5 + - - -
225A BEN 4.0 8.4 - - - -
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Residues in contact with TRP 193 (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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80A THR 4.9 4.3 - - - -
81A LEU* 3.5 27.7 - - + +
152A TYR* 3.6 34.5 - + - -
155A GLN* 3.6 43.3 - - + -
156A ILE* 3.8 19.7 - - + -
160A MET* 3.6 17.2 - - + +
192A SER* 1.3 100.1 - - - +
194A GLY* 1.3 76.4 + - - +
205A VAL* 2.8 53.5 + - + +
225A BEN 3.7 22.9 + - + -
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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