Contacts of the strand formed by residues 147 - 154 (chain B) in PDB entry 5LS6
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 PHE 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.8 7.2 - - + -
97B PHE* 3.7 7.8 - - - -
116B VAL* 3.8 23.3 - - + -
117B GLY 3.9 11.7 + - - +
118B SER 3.3 4.8 + - - -
119B ASN* 3.9 8.5 - - - -
120B ARG* 3.7 28.9 - - - +
121B VAL* 4.5 1.6 - - + -
140B ASP* 3.4 40.4 - - + -
145B GLU* 3.8 17.5 - - + -
146B ASN* 1.3 82.8 + - - +
148B TYR* 1.3 61.1 + - - +
165B VAL* 3.5 35.0 - - + -
166B ALA* 3.5 20.2 - - - +
167B GLY* 3.7 1.6 - - - -
171B ILE 4.8 2.2 - - - -
173B ARG* 3.9 15.0 - - + -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.2 42.5 - + - +
98B GLY* 3.8 0.3 - - - -
116B VAL* 4.0 3.1 - - - -
146B ASN* 3.3 29.6 - - - +
147B PHE* 1.3 76.1 - - - +
149B THR* 1.3 61.8 + - - +
166B ALA 2.8 5.0 + - - +
167B GLY 3.8 0.7 - - - -
168B SER* 3.0 39.6 - - - -
192B ALA* 3.8 11.4 - - + -
193B ILE 3.6 23.8 - - - +
194B ASN* 4.1 8.1 - - - -
365B TYR* 3.3 18.8 + - + +
367B ARG* 4.7 1.0 + - - -
7Q M3L 3.6 51.2 - - - -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 4.7 4.0 - - - -
116B VAL* 3.8 8.1 - - - +
147B PHE 3.8 0.6 - - - -
148B TYR* 1.3 79.5 - - - +
150B CYS* 1.3 67.7 + - - +
165B VAL* 3.4 3.8 - - - +
166B ALA 2.9 32.9 + - - +
193B ILE* 4.2 5.8 - - + +
194B ASN 4.1 5.6 - - - -
195B GLU* 3.5 23.0 + - - +
196B LEU* 3.2 45.9 + - + +
365B TYR* 4.8 0.2 - - - -
367B ARG* 5.0 5.8 + - - -
415B GLN* 5.6 3.8 + - - -
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Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 5.1 1.0 - - - -
99B VAL* 4.5 2.9 - - - -
100B GLN* 3.2 53.6 - - - +
114B ALA* 4.1 13.7 - - - -
116B VAL* 3.9 17.4 - - + +
149B THR* 1.3 80.4 + - - +
151B ALA* 1.3 64.8 + - - +
163B LEU* 4.0 13.9 - - + -
164B ALA 2.8 15.7 - - - +
165B VAL* 3.8 15.3 - - + -
196B LEU* 4.6 4.1 - - - +
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Residues in contact with ALA 151 (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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100B GLN* 4.2 11.9 - - - +
150B CYS* 1.3 77.1 - - - +
152B TRP* 1.3 61.6 + - - +
163B LEU* 3.8 5.2 - - - -
164B ALA* 2.7 41.8 + - + +
196B LEU* 3.9 28.9 - - + +
197B LYS* 4.5 4.5 - - + +
198B PHE* 3.5 18.5 - - + +
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Residues in contact with TRP 152 (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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100B GLN* 2.6 33.6 + - + +
101B PHE 3.2 22.4 - - - +
102B ASN* 3.4 43.2 - - + +
103B TRP 5.1 0.7 - - - +
104B HIS* 3.4 23.9 + - + -
112B VAL* 4.8 6.5 - - + -
113B PHE* 4.1 5.4 - - - -
114B ALA* 3.6 24.8 - - + +
123B LEU* 3.6 25.4 - - + -
151B ALA* 1.3 72.8 - - - +
153B THR* 1.3 63.6 + - - +
161B PRO* 4.2 14.6 - - + -
162B LEU 3.5 13.5 - - - -
163B LEU* 3.6 25.9 - - + +
177B PRO* 4.4 9.2 - - + -
198B PHE* 3.3 13.4 - - - +
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Residues in contact with THR 153 (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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104B HIS* 3.4 23.0 + - - +
152B TRP* 1.3 76.1 - - - +
154B TYR* 1.3 68.4 + - - +
161B PRO* 3.5 5.9 - - - +
162B LEU* 2.7 47.5 + - + +
174B ILE* 6.1 0.9 - - + -
198B PHE* 3.3 40.6 - - + +
203B PRO* 3.0 33.3 + - - +
220B ILE* 4.1 7.4 - - + -
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Residues in contact with TYR 154 (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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63A ARG* 2.5 57.4 + - + +
65A ILE* 4.1 22.9 - - + -
104B HIS* 3.5 31.0 - + + -
153B THR* 1.3 81.1 + - - +
155B ASP* 1.3 60.1 + - - +
156B SER* 3.4 37.3 + - - -
160B HIS 3.2 17.9 - - - +
162B LEU* 3.7 11.7 - - - +
203B PRO* 3.6 43.3 - - + +
204B ASN* 4.8 4.0 - - - +
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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