Contacts of the strand formed by residues 138 - 146 (chain A) in PDB entry 1S3Y
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 LEU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.3 31.5 - - + +
8A THR* 3.9 0.9 - - - -
9A LEU* 3.5 20.9 - - + +
122A VAL* 5.3 0.9 - - + -
132A ALA* 3.5 33.0 - - + +
133A MET* 4.2 16.8 - - - +
135A HIS* 3.5 12.5 + - + +
137A LYS* 1.3 76.1 - - - +
139A ASP* 1.3 58.7 + - - +
140A ARG 3.3 18.8 - - - +
141A ILE* 4.3 2.0 - - + -
169A TRP* 3.3 31.9 - - + -
204A ARG* 4.1 10.0 - - - -
206A LEU* 4.0 6.6 - - - +
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Residues in contact with ASP 139 (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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6A SER* 3.5 23.1 + - - -
7A LEU 3.5 6.6 + - - +
8A THR* 5.0 0.3 + - - -
137A LYS 3.0 6.0 + - - -
138A LEU* 1.3 71.8 - - - +
140A ARG* 1.3 78.2 + - - +
169A TRP* 4.0 6.3 - - - -
203A THR* 3.1 27.8 - - - +
204A ARG* 3.1 16.9 + - - +
206A LEU* 3.3 41.9 - - + +
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Residues in contact with ARG 140 (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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7A LEU 4.0 0.8 + - - +
8A THR* 3.7 19.4 + - + +
9A LEU 3.0 22.5 + - - -
138A LEU* 3.3 5.7 - - - +
139A ASP* 1.3 98.1 + - - +
141A ILE* 1.3 71.4 + - - +
142A MET* 4.3 2.2 - - - -
169A TRP* 4.0 1.6 - - - -
172A GLU* 5.4 0.8 - - - +
180A TRP* 3.3 61.8 - - - +
201A MET* 3.3 34.3 - - + -
202A TRP 3.3 9.9 - - - +
203A THR* 3.4 17.4 - - + +
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Residues in contact with ILE 141 (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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9A LEU* 3.2 31.6 - - + -
11A VAL* 4.3 1.3 - - + -
133A MET* 3.9 21.5 - - + -
138A LEU* 4.3 1.1 - - + -
140A ARG* 1.3 81.8 - - - +
142A MET* 1.3 72.1 + - - +
143A ALA* 3.7 3.8 + - + -
156A PHE* 4.7 2.5 - - + -
160A PHE* 4.0 41.3 - - + -
169A TRP* 3.6 33.7 - - + -
200A GLU 3.9 0.2 - - - +
201A MET* 3.5 5.4 - - - +
202A TRP* 2.7 42.0 + - + +
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Residues in contact with MET 142 (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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8A THR* 3.7 19.3 - - + -
9A LEU 2.6 10.6 + - - +
10A ILE* 3.2 21.7 - - + +
11A VAL* 2.8 27.7 + - - +
35A TYR* 3.8 19.5 - - + +
39A VAL* 3.9 12.8 - - + -
121A PHE* 4.8 0.4 - - + -
140A ARG* 4.3 4.0 - - - -
141A ILE* 1.3 71.7 - - - +
143A ALA* 1.3 59.3 + - - +
177A LEU* 4.7 2.0 - - + -
180A TRP* 3.7 17.7 - - + -
181A VAL* 3.5 22.9 - - + -
200A GLU 3.8 4.5 - - - +
201A MET* 3.4 46.7 - - + +
208A TQT 5.0 0.4 + - - -
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Residues in contact with ALA 143 (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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11A VAL* 3.3 4.5 - - + -
13A LEU* 4.2 5.6 - - + -
35A TYR* 5.7 1.8 - - - -
141A ILE* 3.7 7.3 - - + -
142A MET* 1.3 75.2 - - - +
144A THR* 1.3 64.5 + - - +
145A ILE* 4.0 15.3 - - + -
160A PHE* 3.9 30.5 - - + -
198A GLU 3.9 0.3 - - - +
199A PHE* 3.6 2.8 - - - +
200A GLU* 2.8 40.0 + - - +
202A TRP* 4.6 5.8 - - + +
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Residues in contact with THR 144 (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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11A VAL 2.9 7.0 + - - -
12A ALA* 3.4 14.5 - - + -
13A LEU* 2.8 29.3 + - - +
32A GLU* 2.6 43.0 + - + -
35A TYR* 4.4 3.5 - - - -
143A ALA* 1.3 74.0 - - - +
145A ILE* 1.3 62.5 + - - +
146A ILE* 3.6 5.0 + - + +
197A TYR* 3.9 23.6 - - + -
198A GLU 3.3 11.0 - - - +
199A PHE* 3.5 13.4 - - + -
208A TQT 3.4 4.9 + - - -
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Residues in contact with ILE 145 (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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13A LEU* 3.5 12.8 - - + +
14A THR 4.9 0.9 - - - +
15A THR* 4.1 23.1 - - + +
143A ALA* 4.0 16.4 - - + -
144A THR* 1.3 75.1 - - - +
146A ILE* 1.3 64.1 + - - +
147A TYR* 3.5 31.5 + - + +
161A ARG* 3.5 34.8 - - - +
197A TYR* 3.0 23.9 - - - -
198A GLU* 2.9 15.6 + - + +
200A GLU* 3.3 33.0 - - + +
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Residues in contact with ILE 146 (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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12A ALA* 4.7 7.6 - - + -
13A LEU 2.8 19.1 + - - +
14A THR* 3.3 27.9 - - + -
15A THR 3.5 6.2 + - - -
27A TRP* 3.4 51.4 - - + +
29A LEU* 4.0 12.8 - - + -
144A THR* 4.3 7.0 - - + +
145A ILE* 1.3 73.4 - - - +
147A TYR* 1.3 53.4 + - - +
148A LYS* 2.8 24.5 + - + -
195A PHE* 3.9 27.8 - - + -
196A ASP 3.8 7.2 - - - +
197A TYR* 4.1 11.7 - - + -
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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