Contacts of the strand formed by residues 93 - 100 (chain B) in PDB entry 3S52
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 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.8 21.1 - - + -
76B LEU 3.8 4.0 - - - -
77B ILE* 4.9 4.7 - - + +
78B GLY 4.6 0.2 - - - +
89B VAL* 3.4 18.6 - - + +
90B ALA* 4.1 9.9 + - - +
91B ARG 3.4 5.4 - - - +
92B ALA* 1.3 76.4 - - - +
94B ALA* 1.3 60.6 + - - +
95B GLY 3.7 12.1 - - - +
96B TYR* 3.5 36.3 - - + +
136B VAL* 3.4 18.5 - - + +
168B ILE* 4.0 22.0 - - + -
169B ILE* 4.4 15.0 - - + -
172B ILE* 4.3 7.2 - - + -
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Residues in contact with ALA 94 (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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14B PHE* 3.9 22.9 - - + -
76B LEU* 2.8 25.1 + - + +
78B GLY* 3.6 25.4 - - - -
92B ALA 3.2 1.2 + - - -
93B ILE* 1.3 73.5 - - - +
95B GLY* 1.3 54.6 + - - +
133B PHE* 5.7 0.2 - - - +
135B PRO* 4.1 6.1 - - - +
136B VAL* 3.9 13.2 + - - +
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Residues in contact with GLY 95 (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 VAL* 3.6 5.4 - - - +
76B LEU* 3.0 24.2 + - - +
93B ILE* 3.5 5.5 - - - +
94B ALA* 1.3 80.2 - - - +
96B TYR* 1.3 73.9 + - - -
133B PHE* 4.0 13.2 - - - -
134B ILE 3.3 13.9 - - - -
136B VAL* 3.8 3.8 - - - +
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Residues in contact with TYR 96 (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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73B LEU* 4.1 9.4 - - + -
74B ALA 3.4 5.4 - - - +
75B VAL* 3.8 30.3 - - + -
93B ILE* 3.5 37.6 - - + +
95B GLY* 1.3 75.0 - - - -
97B GLY* 1.3 58.0 + - - +
132B GLY 3.9 0.5 - - - +
133B PHE* 3.2 6.4 - - - -
134B ILE* 2.6 43.6 + - - +
136B VAL* 4.1 20.6 - - + +
139B PHE* 3.4 45.5 - + + -
140B GLY 5.5 2.0 - - - -
142B ALA* 3.3 32.1 - - + +
168B ILE* 4.2 9.2 - - + +
169B ILE* 5.9 0.9 - - - +
208B LEU* 4.8 2.0 - - - -
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Residues in contact with GLY 97 (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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73B LEU* 3.4 13.3 - - - +
74B ALA* 2.9 29.0 + - - -
96B TYR* 1.3 75.2 - - - +
98B VAL* 1.3 61.7 + - - +
130B ILE* 5.7 0.2 - - - -
131B SER* 3.3 11.9 - - - -
132B GLY 3.6 7.4 - - - -
133B PHE* 3.6 9.9 - - - -
208B LEU* 3.9 9.9 - - - -
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Residues in contact with VAL 98 (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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7B TRP* 4.2 8.3 - - + -
54B ILE* 4.5 4.5 - - + +
71B ILE* 3.6 31.2 - - + -
72B GLU 3.4 13.7 - - - +
74B ALA* 4.3 0.9 - - - +
97B GLY* 1.3 75.3 - - - +
99B ALA* 1.3 65.2 + - - +
100B LEU* 5.4 0.4 - - + -
130B ILE* 3.6 2.7 - - - +
131B SER* 2.8 50.5 + - - +
147B LEU* 4.2 7.9 - - + -
206B ILE* 4.0 21.1 - - + -
208B LEU* 4.1 24.5 - - + -
213B VAL* 5.0 2.7 - - + -
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Residues in contact with ALA 99 (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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54B ILE* 4.9 1.1 - - - -
71B ILE* 3.5 0.5 - - - -
72B GLU* 3.0 31.7 + - - +
74B ALA* 4.3 1.1 - - + +
98B VAL* 1.3 77.4 - - - +
100B LEU* 1.3 74.9 + - - +
101B ASP 4.1 0.4 - - - -
128B CYS* 4.1 8.1 - - - -
129B PRO 3.3 13.0 - - - +
130B ILE* 3.8 15.9 - - + -
188B LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 100 (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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54B ILE* 4.1 13.5 - - + -
58B VAL* 5.8 3.4 - - + -
69B HIS* 4.8 4.3 - - + -
70B GLU 3.4 5.4 - - - +
71B ILE* 3.8 27.8 - - + +
99B ALA* 1.3 86.8 - - - +
101B ASP* 1.3 61.0 + - - +
102B LEU* 3.2 28.8 + - + -
127B SER 3.3 9.4 - - - +
128B CYS* 3.5 6.2 - - - +
129B PRO* 3.0 27.0 + - + +
149B LEU* 4.7 8.3 - - + -
198B MSE 4.7 7.0 - - + -
204B LEU* 3.7 29.6 - - + -
206B ILE* 4.2 16.2 - - + -
217B ILE* 5.9 0.2 - - + -
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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