Contacts of the strand formed by residues 137 - 144 (chain A) in PDB entry 2IL1
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 PHE 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ALA* 3.7 5.9 - - - +
136A ASP* 1.3 97.7 - - + +
138A LYS* 1.3 58.1 + - - +
139A LEU* 4.4 11.7 - - + -
185A LYS* 4.5 12.6 - - + -
186A LYS 3.3 2.4 + - - -
187A ILE* 3.3 35.7 - - + -
188A ARG 2.7 31.9 + - - -
301A LEU* 3.6 19.7 - - + -
304A MET* 4.3 22.2 - - + -
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Residues in contact with LYS 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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135A ALA* 5.0 5.6 - - + -
137A PHE* 1.3 77.7 - - - +
139A LEU* 1.3 70.1 + - - +
188A ARG* 3.3 50.0 - - + +
212A LYS* 3.4 13.3 + - - -
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Residues in contact with LEU 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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137A PHE* 4.4 12.6 - - + -
138A LYS* 1.3 84.3 - - - +
140A GLN* 1.3 64.8 + - - +
141A VAL* 5.3 1.6 - - + -
187A ILE* 3.7 24.2 - - + -
188A ARG 3.0 7.1 + - - +
189A LEU* 3.5 13.8 - - + +
190A GLN* 2.8 27.7 + - - +
212A LYS* 3.6 29.8 - - + +
297A VAL* 3.9 22.0 - - + -
300A ILE* 4.2 27.4 - - + -
301A LEU* 4.2 8.7 - - + -
304A MET* 4.4 10.3 - - + -
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Residues in contact with GLN 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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139A LEU* 1.3 75.7 - - - +
141A VAL* 1.3 66.1 + - - +
190A GLN* 3.3 28.5 + - + +
192A TRP* 2.6 34.4 + - + +
207A TYR* 5.5 0.2 - - - -
210A SER* 3.3 44.2 + - - +
211A ALA* 4.3 3.4 - - - -
212A LYS* 2.8 34.0 + - - +
213A GLY 3.5 0.3 + - - -
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Residues in contact with VAL 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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139A LEU 5.2 0.4 - - - -
140A GLN* 1.3 79.0 - - - +
142A ILE* 1.3 67.6 + - - +
189A LEU* 3.9 22.0 - - + -
190A GLN 3.0 9.1 + - - +
191A ILE* 3.8 32.1 - - + -
192A TRP* 2.9 25.5 + - - -
211A ALA* 4.6 0.2 - - - -
213A GLY 3.2 14.8 - - - +
215A ILE* 4.9 3.1 - - + -
293A PHE* 4.5 12.6 - - + -
296A LEU* 4.1 20.6 - - + -
297A VAL* 5.2 2.9 - - + -
300A ILE* 4.1 16.8 - - + -
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Residues in contact with ILE 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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141A VAL* 1.3 80.1 - - - +
143A ILE* 1.3 61.3 + - - +
144A ILE* 3.8 15.9 - - + -
192A TRP* 3.5 29.2 - - + +
194A THR* 4.7 6.5 - - + -
207A TYR* 3.4 23.3 - - + +
208A TYR* 3.7 46.7 - - + -
211A ALA* 3.7 7.9 - - + -
213A GLY 3.0 6.3 + - - -
214A ILE* 3.8 24.5 - - + -
215A ILE* 2.9 29.2 + - - +
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Residues in contact with ILE 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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142A ILE* 1.3 77.2 - - - +
144A ILE* 1.3 61.7 + - - +
151A LYS* 3.7 36.2 - - + +
154A LEU* 5.3 2.7 - - + -
155A MET* 3.6 25.4 - - + +
191A ILE* 3.6 26.7 - - + -
192A TRP 2.9 13.3 + - - +
193A ASP* 4.6 4.2 - - - +
194A THR* 2.9 26.3 + - - -
215A ILE* 3.4 13.9 - - + +
217A VAL* 3.7 22.9 - - + -
293A PHE* 3.8 19.5 - - + -
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Residues in contact with ILE 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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142A ILE* 3.8 17.5 - - + -
143A ILE* 1.3 78.8 - - - +
145A GLY* 1.3 60.4 + - - +
151A LYS* 3.4 13.0 - - - +
194A THR* 3.7 13.2 - - + +
208A TYR* 3.4 37.0 - - + +
214A ILE* 3.5 21.5 - - + -
215A ILE 2.8 16.4 + - - +
216A LEU* 3.5 17.2 - - + -
217A VAL* 2.9 24.8 + - - +
232A TRP* 4.4 11.9 - - + +
236A ILE* 3.8 24.2 - - + -
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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