Contacts of the strand formed by residues 71 - 77 (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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B GLU* 1.3 71.6 - - - +
72B GLU* 1.3 64.5 + - - +
98B VAL* 3.6 18.4 - - + -
99B ALA 3.5 6.7 - - - +
100B LEU* 3.8 12.0 - - + +
147B LEU* 4.4 14.6 - - + -
148B SER 3.3 39.5 - - - +
149B LEU* 4.1 8.7 - - + +
157B GLN* 3.0 40.9 + - + +
191B THR* 2.7 26.6 + - - -
192B PRO* 3.3 13.0 - - + +
206B ILE* 3.6 19.1 - - + -
207B MSE 4.4 0.7 - - - +
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Residues in contact with GLU 72 (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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21B CYS* 5.6 0.7 - - - +
22B VAL 4.5 5.9 + - - +
70B GLU* 3.2 23.0 - - - +
71B ILE* 1.3 82.4 - - - +
73B LEU* 1.3 65.5 + - - +
98B VAL* 3.4 5.7 - - - +
99B ALA 3.0 33.4 + - - +
101B ASP* 3.3 34.6 - - + +
147B LEU* 4.2 8.1 - - - -
188B LEU* 3.4 24.0 - - + +
190B GLY* 2.8 40.1 + - - +
191B THR* 3.8 7.3 + - - +
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Residues in contact with LEU 73 (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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26B TYR* 5.5 0.2 + - - -
72B GLU* 1.3 73.8 - - - +
74B ALA* 1.3 63.3 + - - +
75B VAL* 4.8 2.0 - - + -
96B TYR* 4.1 16.6 - - + -
97B GLY 3.4 17.7 - - - +
139B PHE* 3.9 14.8 - - + -
142B ALA* 3.7 14.1 - - + +
145B ALA* 4.6 3.1 - - + -
147B LEU* 3.9 10.9 - - + +
161B THR* 3.8 19.7 - - + -
164B MSE 4.1 3.1 - - + -
168B ILE* 3.7 30.7 - - + -
188B LEU* 3.8 1.2 - - - -
189B THR* 3.0 41.9 + - - +
190B GLY 4.4 0.6 + - - -
208B LEU* 3.8 22.4 - - + -
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Residues in contact with ALA 74 (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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72B GLU 3.6 0.8 + - - -
73B LEU* 1.3 75.1 - - - +
75B VAL* 1.3 64.2 + - - +
96B TYR* 3.4 7.6 - - - +
97B GLY 2.9 39.9 + - - +
99B ALA* 4.3 5.2 - - + -
130B ILE* 3.7 24.9 - - + -
133B PHE* 4.2 3.6 - - + -
186B ILE* 4.0 3.1 - - + -
187B VAL 3.3 4.3 - - - +
188B LEU* 3.5 22.9 - - + -
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Residues in contact with VAL 75 (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* 4.8 3.8 - - + -
74B ALA* 1.3 79.6 - - - +
76B LEU* 1.3 65.3 + - - +
77B ILE* 3.7 2.9 + - + +
93B ILE* 3.8 31.6 - - + -
95B GLY 3.6 3.1 - - - +
96B TYR* 3.8 19.5 - - + -
133B PHE* 4.1 2.9 - - - -
168B ILE* 4.2 9.4 - - + -
172B ILE* 3.9 20.6 - - + -
186B ILE* 3.3 5.7 - - - +
187B VAL* 2.7 43.5 + - + +
189B THR* 4.0 23.1 - - + -
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Residues in contact with LEU 76 (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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4B HIS* 4.0 33.2 - - + +
12B LEU* 3.9 23.6 - - + -
14B PHE* 3.7 28.5 - - + -
75B VAL* 1.3 72.8 - - - +
77B ILE* 1.3 68.4 + - - +
93B ILE* 3.7 3.3 - - - -
94B ALA* 2.8 36.9 + - + +
95B GLY 3.0 15.3 + - - +
133B PHE* 3.7 27.6 - - + -
184B GLY* 4.0 9.2 - - - +
185B ASP 3.8 10.1 - - - +
186B ILE* 4.3 3.8 - - + -
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Residues in contact with ILE 77 (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* 4.6 0.5 - - - -
75B VAL* 4.5 5.4 - - + +
76B LEU* 1.3 77.8 - - - +
78B GLY* 1.3 56.5 + - - +
79B THR 3.0 27.8 - - - +
81B LEU* 4.0 25.1 - - + -
92B ALA 4.2 2.5 - - - +
93B ILE* 5.0 6.7 - - + -
94B ALA* 4.3 1.1 - - - -
172B ILE* 4.2 26.0 - - + -
181B LEU* 4.2 17.0 - - + +
182B ARG 3.8 15.5 - - - +
184B GLY* 2.7 33.1 + - - -
185B ASP* 2.9 27.2 + - + +
187B VAL* 4.4 13.0 - - + -
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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