Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 5JEI
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.5 0.2 - - - +
110A GLY* 1.3 73.9 - - - +
112A SER* 1.3 67.0 + - - +
143A THR* 3.9 32.5 - - + +
146A PHE* 3.5 38.6 - - + -
147A PHE* 4.1 12.8 - - + -
191A LEU* 4.5 5.8 - - + -
192A LEU 3.7 7.4 - - - +
193A GLU* 4.4 2.0 - - + +
214A ASN* 3.3 3.8 - - - -
215A LEU* 2.8 50.3 + - + -
216A ASP* 2.7 16.5 + - - +
218A LYS* 3.5 26.9 - - - +
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Residues in contact with SER 112 (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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110A GLY 4.0 2.9 - - - -
111A ILE* 1.3 76.8 - - - +
113A ILE* 1.3 64.3 + - - +
114A MET 4.0 0.2 + - - -
191A LEU* 3.3 9.7 - - - +
192A LEU* 2.8 44.3 + - - +
194A SER* 3.3 11.4 - - - -
197A ASN* 2.9 17.8 + - - +
210A LYS* 3.7 16.2 - - - -
213A GLY 4.9 0.9 - - - -
214A ASN* 3.5 19.5 - - - +
215A LEU* 4.2 6.3 - - - -
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Residues in contact with ILE 113 (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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112A SER* 1.3 76.5 - - - +
114A MET* 1.3 68.9 + - - +
115A ILE* 4.1 7.9 - - + -
121A ILE* 4.4 3.1 - - + -
123A SER* 3.4 16.8 - - - +
124A ALA* 3.4 37.0 - - + +
127A LEU* 4.2 17.5 - - + -
189A ALA* 4.5 3.6 - - + -
190A TYR 3.7 4.7 - - - +
191A LEU* 3.9 17.0 - - + -
197A ASN* 3.0 13.2 + - - -
210A LYS* 3.3 0.3 - - - -
211A VAL* 3.1 52.4 + - + +
212A GLY* 5.6 0.2 - - - -
213A GLY 5.3 2.4 + - - +
215A LEU* 4.4 8.5 - - + +
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Residues in contact with MET 114 (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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112A SER 4.0 0.2 + - - -
113A ILE* 1.3 72.5 - - - +
115A ILE* 1.3 66.1 + - - +
178A VAL* 3.9 18.8 - - + -
181A VAL* 4.1 20.3 - - + +
189A ALA* 3.5 8.1 - - - +
190A TYR* 2.8 46.3 + - + +
192A LEU* 3.6 28.3 - - + -
197A ASN* 3.5 21.9 - - - +
200A ILE* 3.9 29.6 - - + -
208A THR* 4.0 26.5 - - - +
209A MET 3.5 5.6 - - - +
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Residues in contact with ILE 115 (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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113A ILE* 4.1 6.9 - - + -
114A MET* 1.3 78.2 - - - +
116A LYS* 1.3 72.4 + - - +
118A GLY 4.6 3.4 - - - +
119A THR* 3.6 42.0 - - + +
121A ILE* 4.2 11.7 - - + +
181A VAL* 3.8 6.3 - - - -
188A TYR 5.2 0.2 - - - -
189A ALA* 4.2 9.6 - - + +
208A THR* 3.2 6.1 - - - -
209A MET* 3.0 51.3 + - + +
211A VAL* 3.3 40.6 - - + -
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Residues in contact with LYS 116 (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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115A ILE* 1.3 73.2 - - - +
117A LYS* 1.3 76.2 + - - +
118A GLY 3.2 0.2 + - - -
119A THR* 2.7 33.7 + - - +
181A VAL* 3.3 35.2 - - + +
182A ARG* 3.7 22.9 - - + +
185A LYS* 5.1 7.1 - - - +
186A GLY* 4.3 17.3 - - - +
188A TYR 4.8 2.9 + - - +
207A ASP* 3.5 35.6 - - - +
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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