Contacts of the strand formed by residues 120 - 127 (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 GLY 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 4.1 2.9 - - - -
118B GLY 3.9 1.6 + - - -
119B SER* 1.3 76.8 - - - +
121B TRP* 1.3 69.7 + - - -
138B THR 3.1 13.2 - - - -
140B ASN 3.6 7.6 - - - -
157B VAL* 3.0 35.2 + - - +
158B TRP* 3.4 14.2 - - - +
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Residues in contact with TRP 121 (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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69B GLN* 3.1 24.4 + - - -
72B ASN* 3.4 43.4 - - + +
73B HIS* 3.4 33.0 - + - -
76B TYR* 4.0 9.9 - - + -
116B LEU* 3.3 7.9 - - - +
120B GLY* 1.3 74.6 - - - -
122B ASN* 1.3 60.1 + - - +
123B TRP* 3.4 26.9 - + + +
137B GLN* 3.4 0.2 - - - -
138B THR* 2.9 41.1 + - - +
140B ASN 2.8 29.7 + - - -
142B GLN 4.1 1.6 - - - -
154B VAL* 3.8 16.2 - - + -
155B VAL 3.6 5.2 - - - -
156B ASP* 3.4 43.5 - - + -
157B VAL* 4.4 0.2 - - - -
158B TRP* 3.5 4.0 - - - +
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Residues in contact with ASN 122 (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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109B PHE* 3.0 59.2 + - - -
112B SER* 2.7 30.7 + - - +
113B ALA* 3.5 28.8 - - + +
116B LEU* 4.6 2.4 - - + +
121B TRP* 1.3 72.7 - - - +
123B TRP* 1.3 61.1 - - - +
135B ILE* 4.2 3.4 - - - +
136B ILE 3.7 2.8 - - - +
137B GLN* 3.7 10.0 - - - +
154B VAL* 3.4 0.6 - - - -
155B VAL* 3.0 35.0 + - + -
157B VAL* 4.8 1.9 - - + +
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Residues in contact with TRP 123 (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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71B TYR* 4.1 6.1 - + - -
72B ASN* 3.1 34.8 - - + -
75B PHE* 4.2 8.1 - + - -
109B PHE* 3.9 5.1 - - - -
121B TRP* 3.4 16.3 - - + +
122B ASN* 1.3 74.3 - - - +
124B ALA* 1.3 65.4 + - - +
125B ALA* 4.6 0.7 - - + +
135B ILE* 3.2 11.8 - - - +
136B ILE* 2.7 47.4 + - + +
138B THR* 3.0 24.3 + - + -
142B GLN 3.9 3.6 - - - -
143B THR* 3.1 23.3 - - - -
144B PRO* 3.2 29.3 - - + +
151B PRO* 3.6 35.0 - - + -
153B LEU 3.2 7.4 - - - +
154B VAL* 3.3 32.8 - - + -
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Residues in contact with ALA 124 (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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105B PHE* 3.9 28.7 - - + -
109B PHE* 4.3 2.7 - - + -
123B TRP* 1.3 73.6 - - - +
125B ALA* 1.3 52.9 + - - +
133B ILE* 4.5 8.5 - - + -
134B GLU 3.2 7.9 - - - -
135B ILE* 4.4 0.9 - - - +
151B PRO* 4.0 0.7 - - - +
152B LEU* 2.7 38.3 + - + +
153B LEU* 2.9 27.8 + - + +
186B VAL* 6.3 0.4 - - + -
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Residues in contact with ALA 125 (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 TRP* 4.0 1.3 - - + -
124B ALA* 1.3 75.0 - - - +
126B TYR* 1.3 62.1 + - - +
127B ASN 3.6 0.9 + - - -
133B ILE* 3.5 0.6 - - - -
134B GLU* 2.7 42.3 + - - +
136B ILE* 3.9 24.0 - - + -
144B PRO* 4.1 20.9 - - + -
149B LYS* 4.1 6.5 - - + -
150B VAL 3.3 14.8 - - - +
151B PRO* 4.3 2.2 - - + -
152B LEU* 4.3 4.7 - - - -
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Residues in contact with TYR 126 (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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125B ALA* 1.3 69.8 - - - +
127B ASN* 1.3 67.9 + - - +
128B LEU* 3.5 31.6 + - + +
131B GLN* 3.2 52.6 + - + +
132B LYS 3.8 11.4 - - - -
133B ILE* 4.2 3.6 - - + +
149B LYS* 3.7 5.7 - - - -
150B VAL* 2.7 36.1 + - + +
152B LEU* 3.9 12.6 - - + +
190B TYR* 3.7 30.3 - + - -
193B ALA* 4.0 26.2 - - + -
194B LYS* 3.8 24.0 - - + +
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Residues in contact with ASN 127 (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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125B ALA 3.6 1.4 + - - -
126B TYR* 1.3 75.2 - - - +
128B LEU* 1.3 55.6 + - - +
129B ASP* 2.8 21.1 + - - +
130B THR* 2.7 43.8 + - - -
131B GLN* 2.7 33.1 + - - -
132B LYS 2.8 19.6 + - - +
134B GLU* 3.2 33.8 + - + +
149B LYS* 3.7 21.3 - - - +
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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