Contacts of the strand formed by residues 136 - 140 (chain B) in PDB entry 4E5Z
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 5.8 5.2 - - + -
129B VAL 3.4 9.4 - - - +
130B GLY* 4.8 0.9 - - - -
134B GLY 4.6 3.6 - - - +
135B ASP* 1.3 73.9 - - - +
137B MET* 1.3 70.2 + - - +
138B LEU* 4.4 8.5 - - + +
148B THR* 5.4 2.2 - - - +
149B PHE* 3.4 10.4 - - - -
150B ILE* 3.0 66.2 + - + +
159B ILE* 3.5 26.9 - - + -
162B LEU* 5.1 16.8 - - + -
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 4.5 21.5 - - - +
109B PRO 5.4 6.5 - - - +
110B PHE* 6.2 2.5 - - + -
128B ALA* 3.4 6.5 - - - +
129B VAL* 3.0 58.7 + - + +
135B ASP 4.3 0.2 + - - -
136B ILE* 1.3 78.1 - - - +
138B LEU* 1.3 61.7 + - - +
139B TRP* 3.5 38.6 + - + +
147B PRO* 3.9 26.9 - - + -
148B THR 3.5 5.2 - - - +
149B PHE* 4.1 17.0 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B HIS* 5.7 3.6 - - + -
126B THR* 3.8 24.7 - - - +
127B VAL 3.9 6.5 - - - +
128B ALA* 4.5 11.4 - - + +
136B ILE* 4.3 8.9 - - + +
137B MET* 1.3 70.4 - - - +
139B TRP* 1.3 61.4 + - - +
140B ASN* 3.9 4.1 + - + +
147B PRO* 3.7 4.0 - - - +
148B THR* 3.0 55.2 + - + +
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Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 3.5 37.5 - - + -
107B ALA* 4.2 5.4 - - - -
108B ALA* 4.0 35.7 - - + -
125B SER 3.9 0.9 - - - +
126B THR* 3.4 1.5 - - - -
127B VAL* 2.7 57.4 + - + +
129B VAL* 6.0 0.7 - - + -
137B MET* 3.5 29.2 + - + -
138B LEU* 1.3 73.6 - - - +
140B ASN* 1.3 82.6 + - - +
141B PHE* 3.3 31.9 - + + +
145B ASP 5.7 1.5 + - - -
147B PRO* 3.8 23.5 - - + +
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Residues in contact with ASN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B HIS* 3.4 8.7 + - - -
125B SER* 2.5 27.9 + - - -
126B THR* 3.1 30.3 - - + +
138B LEU* 3.9 6.9 + - + +
139B TRP* 1.3 88.2 + - - +
141B PHE* 1.3 85.8 + - - +
143B ILE* 3.1 40.2 - - + +
145B ASP 4.9 0.5 - - - +
147B PRO* 5.6 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