Contacts of the strand formed by residues 117 - 124 (chain B) in PDB entry 3D87
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 ARG 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 3.5 18.5 - - - +
112B LYS 4.6 2.4 + - - -
113B ASN* 4.1 13.2 + - - +
115B SER* 3.1 34.4 + - - +
116B GLY* 1.3 78.9 - - - +
118B PHE* 1.3 57.7 + - - +
170B GLU* 3.9 26.0 - - + +
171B CYS 3.0 14.8 - - - +
172B GLN* 2.7 28.0 + - + +
207B ILE* 4.4 0.6 - - - +
239B THR* 6.0 2.8 - - - +
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Residues in contact with PHE 118 (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 CYS* 4.3 1.3 - - + -
110B GLU 3.4 15.0 - - - +
111B ALA* 4.0 3.1 - - + +
116B GLY 4.1 9.0 - - - -
117B ARG* 1.3 75.7 - - - +
119B THR* 1.3 64.0 + - - +
120B CYS* 3.5 27.1 - - - -
136B SER* 3.6 18.8 - - - -
146B VAL* 3.9 11.4 - - + -
170B GLU* 3.6 2.6 - - - +
171B CYS* 2.9 64.4 + - + +
173B GLU* 5.2 1.8 - - + -
186B ILE* 3.9 20.4 - - + -
188B VAL* 3.6 9.4 - - + -
205B PHE* 3.9 9.6 - + - -
207B ILE* 4.2 12.3 - - + -
210B ILE* 3.7 19.5 - - + -
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Residues in contact with THR 119 (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 CYS* 3.1 2.5 - - - +
110B GLU 2.9 28.5 + - - -
117B ARG* 5.9 0.2 - - - +
118B PHE* 1.3 75.3 - - - +
120B CYS* 1.3 68.9 + - - +
121B TRP* 3.3 44.7 - - + -
168B SER* 4.0 11.2 - - - +
169B VAL 3.1 19.1 - - - +
170B GLU* 2.4 33.2 + - + +
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Residues in contact with CYS 120 (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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107B LEU* 5.1 4.7 - - + -
108B ARG 3.6 6.5 - - - +
109B CYS* 3.1 34.8 - - - +
118B PHE* 3.5 26.5 - - - -
119B THR* 1.3 74.3 - - - +
121B TRP* 1.3 63.4 + - - +
122B TRP* 3.8 16.9 - - + -
168B SER* 3.0 25.6 - - - -
169B VAL* 3.3 14.4 + - + -
171B CYS* 4.9 0.4 - - - -
188B VAL* 4.1 18.6 - - + -
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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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98B GLN* 3.6 8.1 - - - +
107B LEU* 3.9 1.0 - - - -
108B ARG* 2.8 70.6 + - - +
110B GLU* 3.2 36.6 - - + -
112B LYS* 4.8 15.9 - - + -
119B THR* 3.3 52.0 - - + -
120B CYS* 1.3 73.8 - - - +
122B TRP* 1.3 62.4 + - - +
154B SER* 3.9 7.7 + - - -
166B GLU* 3.1 36.8 + - + +
167B TYR 3.3 12.6 - - - +
168B SER* 3.8 7.1 + - - -
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Residues in contact with TRP 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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95B LEU* 3.0 37.7 - - + -
98B GLN* 4.2 2.0 - - - -
106B PHE 2.8 24.2 - - - +
107B LEU* 4.6 4.5 - - + -
120B CYS* 3.8 15.7 - - + -
121B TRP* 1.3 76.5 - - - +
123B LEU* 1.3 65.6 + - - +
132B PHE* 3.2 27.5 - + + -
134B VAL* 3.9 9.9 - - + -
151B ALA* 3.1 35.4 - - + -
165B TYR 3.5 0.9 - - - +
166B GLU* 3.5 6.2 - - - +
167B TYR* 2.9 55.6 + + + +
168B SER* 4.2 3.6 - - - -
169B VAL* 3.4 31.9 - - + -
190B VAL* 4.1 19.7 - - + -
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Residues in contact with LEU 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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95B LEU* 3.1 7.5 - - - +
96B LYS* 2.3 61.2 + - + +
98B GLN* 3.8 34.2 + - + +
106B PHE 4.1 2.8 + - - -
122B TRP* 1.3 78.0 - - - +
124B THR* 1.3 58.7 + - - +
157B ARG* 5.0 1.6 - - - +
164B GLU* 2.8 45.5 - - - +
165B TYR 4.0 1.6 - - - +
166B GLU* 3.2 38.1 - - + +
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Residues in contact with THR 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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94B ILE* 2.7 27.5 + - - +
95B LEU* 4.2 8.3 - - - -
96B LYS* 4.4 2.2 - - - +
123B LEU* 1.3 77.2 - - - +
125B THR* 1.3 63.4 + - - +
126B ILE* 3.4 34.4 + - - +
130B LEU* 3.5 16.2 - - + -
132B PHE* 4.8 0.7 - - + -
164B GLU* 3.4 5.0 - - - +
165B TYR* 2.4 48.2 + - + +
167B TYR* 3.5 21.1 - - + -
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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