Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 3CEI
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.3 5.2 - - + -
94B ALA* 3.9 25.4 - - + -
95B LEU* 3.8 25.8 - - + -
98B ASP* 2.9 21.9 + - - +
99B PHE* 3.4 34.0 - - + -
105B PHE* 4.9 0.2 - - + -
124B ALA* 4.5 9.2 - - + -
125B ALA 3.5 11.7 - - - +
126B TYR* 4.2 3.4 - - + -
132B LYS* 1.3 76.6 - - - +
134B GLU* 1.3 67.1 + - - +
152B LEU* 3.8 30.1 - - + -
190B TYR* 4.0 16.6 - - + -
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Residues in contact with GLU 134 (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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99B PHE* 4.6 0.7 - - - -
124B ALA* 3.2 4.0 - - - -
125B ALA 2.7 43.5 + - - +
127B ASN* 3.2 25.7 + - + +
130B THR* 4.9 2.9 + - + +
132B LYS* 4.2 12.3 - - + +
133B ILE* 1.3 76.4 - - - +
135B ILE* 1.3 64.6 + - - +
136B ILE* 3.6 13.5 + - + +
149B LYS* 2.6 42.6 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.5 34.4 - - + -
105B PHE* 3.8 17.9 - - + -
108B ASP* 3.6 12.1 - - + -
109B PHE* 3.5 32.1 - - + +
112B SER* 3.7 32.0 + - - +
122B ASN* 4.2 9.0 - - - +
123B TRP 3.2 11.9 - - - +
124B ALA* 5.0 0.4 - - - -
134B GLU* 1.3 73.1 - - - +
136B ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 136 (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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122B ASN* 3.7 3.6 - - - +
123B TRP* 2.7 41.7 + - + +
125B ALA* 3.9 18.4 - - + -
134B GLU* 3.6 33.9 - - + +
135B ILE* 1.3 79.7 - - - +
137B GLN* 1.3 71.7 + - - +
138B THR* 4.0 15.3 - - + -
144B PRO* 4.2 15.3 - - + -
147B ASP* 5.9 2.9 - - - +
149B LYS* 3.6 23.1 - - + +
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Residues in contact with GLN 137 (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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112B SER* 2.9 36.3 + - - +
115B THR* 4.1 6.7 + - - +
116B LEU* 3.3 37.3 - - + +
121B TRP 3.4 3.8 - - - -
122B ASN* 3.7 7.0 - - - +
135B ILE 4.4 0.2 + - - -
136B ILE* 1.3 80.7 - - - +
138B THR* 1.3 63.1 + - - +
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Residues in contact with THR 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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116B LEU* 3.7 5.5 - - - +
120B GLY* 3.1 3.6 - - - -
121B TRP* 2.9 37.6 + - - +
123B TRP* 3.0 29.6 + - + +
136B ILE* 4.0 11.9 - - + -
137B GLN* 1.3 78.4 - - - +
139B SER* 1.3 59.6 + - - +
142B GLN* 2.7 35.0 + - + +
143B THR* 4.3 2.9 - - - +
144B PRO* 4.1 14.8 - - + -
147B ASP* 6.0 1.1 - - - +
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Residues in contact with SER 139 (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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139A SER* 5.7 0.7 + - - -
140A ASN* 4.8 9.0 + - - -
116B LEU* 5.0 4.7 - - - -
117B PHE 5.7 1.8 - - - -
119B SER 3.6 7.5 + - - -
138B THR* 1.3 75.2 - - - +
140B ASN* 1.3 85.5 + - - +
141B ALA 3.0 4.2 + - - -
142B GLN* 3.0 24.9 + - - +
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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