Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 4ISL
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 3.3 3.2 + - - -
134A LYS* 1.3 84.3 + - - +
136A ILE* 1.3 64.3 + - - +
137A TRP* 4.9 4.4 + - - +
159A GLU* 3.5 32.3 - - + +
160A ILE 3.3 6.5 - - - +
161A ARG* 3.8 25.6 - - + +
201A SER* 5.5 0.2 - - - -
202A VAL 5.5 0.5 + - - -
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Residues in contact with ILE 136 (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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130A PHE* 5.4 1.6 - - + -
134A LYS* 4.1 18.2 - - + +
135A ALA* 1.3 78.9 - - - +
137A TRP* 1.3 69.9 + - - +
159A GLU* 3.4 5.4 - - - +
160A ILE* 2.7 38.3 + - + +
162A VAL* 3.9 14.6 - - + -
181A MET* 5.3 1.1 - - + -
183A VAL* 3.7 27.8 - - + -
199A LEU* 4.0 27.1 - - + -
200A SER 3.4 9.9 - - - +
201A SER* 3.5 29.4 - - - +
210A ALA* 4.1 13.7 - - + -
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Residues in contact with TRP 137 (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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20A THR* 5.7 0.9 - - - -
27A TRP* 3.6 29.6 - + + -
135A ALA* 4.9 3.1 + - - +
136A ILE* 1.3 80.9 - - - +
138A VAL* 1.3 62.1 + - - +
139A THR* 5.2 1.1 + - + -
157A LYS* 3.7 35.0 - - + -
158A GLY* 3.5 12.1 - - - -
159A GLU* 3.6 56.1 + - + +
160A ILE* 4.8 0.2 - - - -
198A PRO 3.9 1.0 - - - +
199A LEU* 3.4 10.1 - - - +
200A SER* 2.8 47.5 + - - +
202A VAL* 5.3 9.7 - - + +
304A GOL 3.4 36.8 + - - -
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Residues in contact with VAL 138 (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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16A VAL* 4.4 16.2 - - + +
136A ILE 4.3 0.2 + - - -
137A TRP* 1.3 75.0 - - - +
139A THR* 1.3 67.6 + - - +
157A LYS* 3.4 3.6 - - - +
158A GLY* 2.9 43.6 + - - +
160A ILE* 3.8 24.4 - - + +
189A ASP 4.7 2.2 - - - +
190A SER* 3.8 21.1 - - - +
194A ASP* 5.4 0.2 - - + -
198A PRO 4.2 4.3 - - - +
199A LEU* 4.1 3.1 - - + -
213A VAL* 3.7 30.7 - - + -
228A TYR* 3.8 15.3 - - + +
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Residues in contact with THR 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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16A VAL* 4.0 5.6 - - - -
27A TRP* 3.6 49.9 - - + +
29A TRP* 5.7 0.5 + - - -
30A GLN* 2.6 34.1 + - - +
137A TRP* 5.2 1.1 - - + -
138A VAL* 1.3 88.2 - - - +
140A GLY* 1.3 58.9 + - - +
155A LEU* 4.4 4.9 - - - -
156A GLN 3.1 13.2 - - - +
157A LYS* 3.8 4.5 - - + -
194A ASP* 4.3 6.8 - - - +
197A GLY* 4.7 8.1 - - - -
198A PRO* 4.0 14.4 + - - +
200A SER* 5.0 3.8 + - - +
213A VAL* 5.1 0.2 - - - +
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Residues in contact with GLY 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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16A VAL* 3.8 2.8 + - - +
30A GLN* 4.5 5.2 - - - -
139A THR* 1.3 75.7 - - - +
141A TRP* 1.3 62.2 + - - -
142A GLY 3.4 4.9 + - - -
155A LEU* 3.5 15.0 - - - +
156A GLN* 2.9 36.8 + - - +
194A ASP* 3.3 14.4 - - - -
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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