Contacts of the strand formed by residues 109 - 121 (chain B) in PDB entry 4SBV
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 LYS 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TYR* 4.0 29.0 - - + +
191A GLU 2.9 29.7 + - - -
192A VAL* 4.6 0.7 - - - +
193A SER* 3.4 30.3 - - - +
221A PRO 5.5 2.2 - - - -
107B TRP* 3.9 7.4 - - - +
108B SER* 1.3 82.2 - - - +
110B TYR* 1.3 64.5 + - - +
196B ARG* 4.5 8.0 - - + +
197B TYR 3.4 24.7 - - - +
198B PRO* 3.7 10.5 - - + -
199B PHE* 5.4 0.7 - - - +
251B ILE* 3.2 33.7 + - + +
252B GLU* 2.9 29.5 + - - -
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Residues in contact with TYR 110 (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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92B MET* 4.0 7.6 - - + +
93B PRO* 3.3 38.6 - - + +
104B ALA* 6.1 1.3 - - + -
109B LYS* 1.3 78.4 - - - +
111B ALA* 1.3 88.9 - - - +
112B TRP* 3.8 27.1 + + - -
196B ARG* 3.7 5.3 - - - +
197B TYR* 2.8 60.9 + + + +
198B PRO 3.6 23.7 + - - -
199B PHE* 4.5 7.2 - + + -
219B LEU 4.8 2.6 + - - -
221B PRO* 3.8 17.2 - - - +
248B ILE* 3.4 26.0 - - + -
249B ARG 3.4 10.8 - - - +
250B LEU* 4.2 5.8 - - + -
251B ILE* 4.1 3.3 - - - +
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Residues in contact with ALA 111 (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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110B TYR* 1.3 87.6 - - - +
112B TRP* 1.4 65.4 + - - +
113B VAL* 4.9 0.9 - - + -
195B LYS 4.2 17.5 - - - +
196B ARG* 4.2 13.0 - - + +
197B TYR* 5.1 2.5 - - - +
248B ILE* 3.6 1.4 - - - +
249B ARG* 2.6 58.3 + - + +
251B ILE* 5.6 0.2 - - + -
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Residues in contact with TRP 112 (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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91B VAL* 2.7 27.4 + - + +
92B MET 4.0 2.0 - - - -
93B PRO* 3.7 23.6 - - + -
96B VAL* 4.2 5.4 - - + -
100B LEU* 3.7 22.4 - - + -
110B TYR* 3.8 19.1 - + - -
111B ALA* 1.4 73.0 - - - +
113B VAL* 1.3 64.0 + - - +
114B ALA 4.2 3.8 - - - +
115B ILE* 3.7 36.8 - - + -
187B LEU* 4.4 10.8 - - + -
189B THR* 3.4 26.5 - - + +
192B VAL* 6.2 0.7 - - + -
197B TYR* 5.4 2.5 - + - -
221B PRO* 3.7 20.1 - - + +
246B TYR* 3.4 28.9 - + + -
248B ILE* 3.9 22.0 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 5.7 4.9 - - + -
111B ALA* 3.4 0.8 + - + -
112B TRP* 1.3 77.5 - - - +
114B ALA* 1.3 64.9 - - + +
189B THR* 3.7 15.2 + - - +
247B THR* 2.7 35.9 + - + +
248B ILE 4.4 1.3 - - - +
249B ARG* 4.0 27.6 - - + +
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Residues in contact with ALA 114 (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 TRP* 4.2 3.1 - - - -
113B VAL* 1.3 89.1 - - + +
115B ILE* 1.3 64.7 - - - +
189B THR* 4.7 3.6 - - - -
245B SER 4.2 1.8 - - - +
246B TYR* 3.0 5.1 - - - +
247B THR* 2.6 44.7 + - - +
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Residues in contact with ILE 115 (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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91B VAL* 3.8 22.2 - - + -
96B VAL* 4.0 17.3 - - + -
112B TRP* 3.7 38.1 - - + -
114B ALA* 1.3 75.9 - - - +
116B ARG* 1.3 64.8 + - - +
117B TYR* 4.0 15.8 - - + +
186B ALA* 3.4 4.7 - - - +
187B LEU* 3.3 56.6 + - + +
189B THR* 5.1 1.4 - - - +
244B ALA* 4.9 2.7 - - + -
245B SER 3.5 4.9 - - - +
246B TYR* 3.7 17.9 - - + -
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Residues in contact with ARG 116 (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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115B ILE* 1.3 81.8 - - - +
117B TYR* 1.3 67.6 + - - +
118B THR* 3.6 6.1 + - - +
170B PHE* 3.3 43.9 - - - -
184B THR* 2.9 35.4 + - - +
185B ILE 3.3 8.7 - - - +
186B ALA* 3.8 25.9 - - + +
243B TYR 3.6 0.7 - - - +
244B ALA* 3.3 5.0 - - - -
245B SER* 3.0 43.7 + - - +
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Residues in contact with TYR 117 (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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75B SER* 3.7 26.9 - - - -
89B GLU* 4.9 4.9 + - + -
90B LEU 4.2 2.1 + - - -
91B VAL* 3.2 41.0 - - + +
96B VAL* 3.3 21.1 - - + +
115B ILE* 4.2 11.4 - - + -
116B ARG* 1.3 75.0 - - - +
118B THR* 1.3 63.6 + - - +
133B MET* 4.5 1.7 - - - +
135B PHE* 4.4 15.0 - + - -
184B THR* 2.9 15.4 + - - -
185B ILE* 2.7 41.7 + - + +
224B LEU* 3.5 32.0 - - + +
242B LEU* 3.3 25.1 - - + -
243B TYR 3.4 3.8 - - - -
244B ALA* 4.8 6.3 - - + -
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Residues in contact with THR 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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116B ARG* 3.6 14.0 + - - +
117B TYR* 1.3 78.0 - - - +
119B TYR* 1.3 66.9 - - - +
120B LEU* 4.9 1.3 - - + -
133B MET* 6.0 0.7 - - - -
167B GLY* 4.1 20.6 - - - +
170B PHE* 3.7 21.6 - - + +
171B VAL* 5.2 8.1 - - + -
183B ILE 3.6 7.2 - - - +
184B THR* 3.1 26.7 + - - +
242B LEU* 2.8 7.8 - - - +
243B TYR* 2.7 39.7 + - - -
245B SER* 4.5 3.7 + - - -
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Residues in contact with TYR 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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78B LEU* 3.8 23.1 - - + -
118B THR* 1.3 75.6 - - - +
120B LEU* 1.3 91.7 + - - +
121B PRO* 3.6 16.4 - - + -
131B ILE* 3.1 36.8 - - + -
133B MET* 5.8 1.1 - - - -
161B VAL* 2.6 37.4 + - + +
163B GLU 3.7 13.7 - - - -
164B GLY* 3.5 9.8 - - - +
183B ILE* 3.1 36.2 + - + +
228B MET* 4.9 0.9 - - + -
239B THR* 2.8 21.5 + - - -
240B GLY* 3.2 11.6 + - - -
241B ARG 3.2 14.1 - - - -
242B LEU* 4.3 4.0 - - + +
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Residues in contact with LEU 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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118B THR* 4.9 1.8 - - + -
119B TYR* 1.3 93.3 - - - +
121B PRO* 1.3 76.9 - - + +
122B SER* 4.3 1.7 - - - -
164B GLY 3.6 8.7 - - - +
165B GLN* 4.3 8.1 - - + +
167B GLY* 3.9 4.0 - - - -
168B LEU* 3.5 45.5 - - + +
171B VAL* 3.5 27.1 - - + -
240B GLY* 3.5 2.3 - - - -
241B ARG* 2.8 31.5 + - - +
243B TYR* 3.8 29.6 - - + +
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Residues in contact with PRO 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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119B TYR* 3.6 6.9 - - + -
120B LEU* 1.3 91.5 - - + +
122B SER* 1.3 60.8 - - - +
123B CYS 4.8 2.2 - - - +
161B VAL 3.6 3.1 - - - +
162B TRP* 3.2 44.0 - - - +
163B GLU 3.3 19.7 - - - +
164B GLY 3.6 1.3 - - - -
165B GLN* 3.5 34.8 - - + +
239B THR 4.0 1.3 - - - +
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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