Contacts of the strand formed by residues 136 - 140 (chain F) in PDB entry 3EI4
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 136 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F VAL 3.4 7.0 - - - +
130F GLY* 4.9 0.9 - - - -
134F GLY 3.6 7.6 - - - +
135F ASP* 1.3 73.5 - - - +
137F MET* 1.3 63.7 + - - +
138F LEU 4.6 0.2 - - - +
148F THR 3.8 0.2 - - - +
149F PHE* 3.4 8.8 - - - -
150F ILE* 2.9 59.0 + - + +
159F ILE* 3.6 31.2 - - + -
162F LEU* 4.5 11.4 - - + -
172F PHE* 3.9 24.0 - - + -
182F ARG* 3.8 18.2 - - - +
186F PHE* 3.9 28.5 - - + -
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Residues in contact with MET 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ALA* 5.0 6.1 - - + -
109F PRO 3.1 28.5 - - - +
110F PHE* 4.1 23.3 - - + -
127F VAL 3.5 1.0 - - - +
128F ALA* 3.2 6.2 - - - +
129F VAL* 2.9 38.3 + - + +
135F ASP 4.2 0.2 - - - -
136F ILE* 1.3 76.1 - - - +
138F LEU* 1.3 61.5 + - - +
139F TRP* 3.5 36.3 - - + -
147F PRO* 3.6 29.2 - - + -
148F THR 3.5 3.4 - - - +
149F PHE* 4.3 9.9 - - + -
415F ILE* 4.1 13.9 - - + -
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F THR* 3.4 34.3 - - + -
127F VAL 3.6 4.9 - - - +
136F ILE* 4.1 1.4 - - - +
137F MET* 1.3 69.7 - - - +
139F TRP* 1.3 58.2 + - - +
140F ASN* 3.9 4.5 + - + +
147F PRO* 3.4 4.4 - - - +
148F THR* 2.8 52.0 + - - +
164F PHE* 3.8 11.9 - - + -
169F THR 5.8 0.2 - - - +
186F PHE* 3.4 50.5 - - + -
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Residues in contact with TRP 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LYS* 4.1 25.5 - - + +
107F ALA 4.0 11.9 - - - -
108F ALA* 3.6 29.8 - - + -
125F SER 3.3 4.7 - - - +
126F THR* 4.3 1.1 - - - -
127F VAL* 2.7 47.4 + - + +
137F MET* 3.5 34.7 - - + -
138F LEU* 1.3 71.5 - - - +
140F ASN* 1.3 73.0 + - - +
141F PHE* 3.4 31.2 + + + +
144F LYS* 5.9 1.6 - - - +
145F ASP 6.4 0.2 - - - -
147F PRO* 3.8 21.6 - - + +
415F ILE* 3.9 28.3 - - + -
417F ILE* 4.2 14.6 - - + -
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Residues in contact with ASN 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F HIS* 5.0 2.8 - - - +
125F SER* 3.5 21.2 - - - -
126F THR* 3.3 26.0 + - + +
138F LEU* 3.9 6.5 + - + +
139F TRP* 1.3 81.0 + - - +
141F PHE* 1.3 84.6 + - - +
142F GLY 4.0 2.4 + - - -
143F ILE* 2.7 59.3 - - + +
144F LYS 4.4 0.9 + - - -
145F ASP 5.2 0.3 + - - -
147F PRO* 5.4 0.8 - - - +
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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