Contacts of the strand formed by residues 149 - 157 (chain C) 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 SER 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C GLN 3.7 0.2 - - - +
145C TYR* 2.7 45.2 + - - +
146C SER* 4.6 7.1 - - - -
148C ASN* 1.3 82.5 + - - +
150C TRP* 1.3 70.2 + - - +
151C ARG* 4.1 15.1 + - - -
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Residues in contact with TRP 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 3.6 35.9 - + - -
103C TYR* 4.4 10.0 - + - -
105C PHE* 4.4 5.8 - + - -
142C TYR* 3.8 18.1 - - + -
143C GLN 3.2 27.1 - - - +
144C LYS* 3.5 34.3 - - + -
147C GLN 5.5 1.8 - - - -
148C ASN* 3.2 25.4 + - - +
149C SER* 1.3 79.6 + - - +
151C ARG* 1.3 72.7 + - - +
152C TYR 4.3 0.2 + - - -
188C PHE 3.9 13.9 - - - -
189C ARG* 3.4 63.9 - - + +
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Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C TYR* 3.3 4.5 - - - -
143C GLN* 2.9 30.3 + - + +
145C TYR* 3.5 40.6 - - + -
149C SER* 4.1 12.5 + - - -
150C TRP* 1.3 83.6 + - - +
152C TYR* 1.3 69.3 + - - +
153C LEU* 3.8 1.8 - - + +
136D GLU* 4.1 20.0 + - - +
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Residues in contact with TYR 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLU* 4.1 26.9 - - + -
141C LEU 4.3 1.6 - - - -
142C TYR* 3.6 29.9 - + + -
151C ARG* 1.3 81.9 - - - +
153C LEU* 1.3 95.1 + - - +
154C SER* 3.8 9.6 - - - -
155C ASN* 3.0 32.1 + - + +
138D HIS* 3.3 42.8 - + + +
140D GLU* 5.5 2.7 - - - -
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 2.9 32.1 + - + +
142C TYR 3.3 32.1 - - - +
143C GLN* 3.6 31.2 - - + +
145C TYR* 5.8 0.2 - - + -
151C ARG* 4.1 0.7 - - + +
152C TYR* 1.3 99.4 - - - +
154C SER* 1.3 64.5 + - - +
171C VAL* 4.7 3.8 - - + -
174C VAL* 4.3 15.0 - - + -
188C PHE* 4.3 13.9 - - + -
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Residues in contact with SER 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 3.2 35.5 + - - +
152C TYR* 3.7 10.5 + - - -
153C LEU* 1.3 82.3 - - - +
155C ASN* 1.3 64.5 + - - +
156C ARG* 5.8 2.0 - - - -
169C PHE* 3.5 26.0 - - - +
170C ASP 5.7 2.4 + - - -
171C VAL* 6.0 0.2 - - - +
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C HIS* 3.0 38.2 + - - -
139C VAL 2.8 23.3 + - - -
140C GLU* 3.4 17.4 - - - +
152C TYR* 3.0 20.3 + - + +
154C SER* 1.3 74.9 - - - +
156C ARG* 1.3 79.2 + - - +
157C LEU* 4.0 5.5 - - - +
169C PHE* 4.4 4.2 - - - -
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Residues in contact with ARG 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA* 4.6 15.2 - - - +
139C VAL* 3.5 20.5 + - - +
154C SER* 5.4 2.2 + - - -
155C ASN* 1.3 85.0 + - - +
157C LEU* 1.3 74.1 + - - +
158C LEU* 3.3 16.0 - - + +
167C LEU* 4.1 18.5 - - + +
168C SER* 2.3 41.6 + - - +
169C PHE* 3.5 41.7 - - + +
170C ASP* 4.9 4.2 - - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLU* 4.2 17.7 - - + +
137C GLN 4.4 5.4 - - - +
138C HIS* 3.4 33.4 - - + +
155C ASN* 4.0 5.4 - - - +
156C ARG* 1.3 87.3 - - - +
158C LEU* 1.3 62.2 + - - +
167C LEU* 5.3 0.9 - - - +
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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