Contacts of the strand formed by residues 153 - 160 (chain B) in PDB entry 5FFO
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 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL 3.8 4.3 - - - -
118B LEU* 5.1 2.9 - - + -
142B LEU 4.8 2.2 - - - -
143B SER* 5.0 4.9 - - - -
146B MET* 3.4 54.5 - - + +
147B SER* 4.7 11.2 - - - +
150B THR* 4.2 19.1 - - + +
151B SER 3.2 8.1 + - - +
152B ASN* 1.3 74.3 + - - +
154B ARG* 1.3 68.1 + - - +
155B LEU* 3.5 55.2 - - + -
201B ASN* 3.4 24.9 - - - +
203B ALA* 4.2 17.3 - - + -
242B ARG* 3.8 0.8 - - - +
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Residues in contact with ARG 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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116B VAL 3.4 5.5 + - - +
117B ASP* 3.3 12.6 - - - +
118B LEU 3.2 19.2 + - - -
152B ASN* 4.6 3.2 + - - -
153B PHE* 1.3 81.6 - - - +
155B LEU* 1.3 61.2 + - - +
199B LEU* 3.7 24.8 + - + +
200B THR* 3.2 17.3 - - - +
201B ASN* 3.5 32.8 - - + +
242B ARG* 3.2 37.1 - - - +
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Residues in contact with LEU 155 (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 LEU* 3.1 16.4 - - + +
142B LEU* 3.7 21.8 - - + -
143B SER* 4.6 4.9 - - - -
153B PHE* 3.5 36.3 - - + -
154B ARG* 1.3 73.3 - - - +
156B GLY* 1.3 60.2 + - - +
197B LEU* 4.1 6.1 - - - +
198B PRO 4.0 1.9 - - - +
199B LEU* 3.4 5.8 - - - -
200B THR* 3.0 31.3 + - - +
201B ASN 5.0 0.2 - - - +
202B ASP 4.3 1.3 - - - +
203B ALA* 4.2 11.2 - - - -
206B PHE* 3.5 50.7 - - + -
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Residues in contact with GLY 156 (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 LEU 3.0 10.2 + - - +
119B TYR* 4.1 6.7 - - - -
120B TYR* 3.2 19.0 + - - +
155B LEU* 1.3 73.9 - - - +
157B PHE* 1.3 63.6 + - - +
197B LEU* 3.3 19.5 - - - -
198B PRO 4.1 0.4 - - - -
199B LEU* 3.6 14.0 - - - +
206B PHE* 3.5 13.2 - - - -
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Residues in contact with PHE 157 (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* 2.7 22.9 + - - -
120B TYR* 3.2 34.1 - + + -
122B MET* 3.5 49.4 - - + -
156B GLY* 1.3 75.5 - - - +
158B GLY* 1.3 67.7 + - - +
159B SER* 4.2 3.8 - - - -
196B ILE* 3.3 21.9 + - + -
197B LEU* 2.8 40.3 + - + +
206B PHE* 4.1 13.0 - + + -
209B ILE* 3.7 18.8 - - + -
210B VAL* 4.7 5.8 - - + -
213B GLN* 3.2 31.6 - - + -
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Residues in contact with GLY 158 (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* 3.2 17.8 + - - -
120B TYR 2.9 8.8 + - - +
121B LEU* 3.4 8.6 - - - -
122B MET 2.9 24.8 + - - -
157B PHE* 1.3 84.2 - - - +
159B SER* 1.3 61.9 + - - -
193B PHE* 4.1 2.7 - - - -
194B LYS 3.5 10.5 - - - -
196B ILE 4.2 0.7 - - - -
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Residues in contact with SER 159 (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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122B MET 3.4 5.8 - - - -
124B LEU* 3.5 30.6 - - - +
157B PHE* 4.2 13.0 - - - -
158B GLY* 1.3 74.8 - - - -
160B PHE* 1.3 61.3 + - - +
191B PHE* 3.5 13.0 - - - -
193B PHE* 3.1 6.3 - - - -
194B LYS* 2.8 37.4 + - - +
196B ILE* 3.4 19.6 - - - +
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Residues in contact with PHE 160 (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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121B LEU* 3.9 12.3 - - + -
122B MET 3.3 23.0 + - - -
123B ASP* 3.5 29.6 - - + -
124B LEU* 3.0 26.2 + - - +
159B SER* 1.3 75.5 - - - +
161B VAL* 1.3 73.1 + - - +
191B PHE* 3.7 3.6 - - - -
192B GLY 3.1 17.7 - - - +
193B PHE* 4.2 0.7 - - - -
223B GLU* 4.2 8.7 - - + -
224B GLY 3.6 16.8 - - - +
225B GLY* 3.6 14.8 - - - -
228B ALA* 3.8 26.7 - - + -
251B PHE* 3.5 34.1 - + - -
252B VAL 4.0 2.9 - - - -
253B SER* 4.1 2.2 - - - -
257B SER* 6.0 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