Contacts of the strand formed by residues 138 - 145 (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 HIS 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLN* 1.3 75.1 - - - +
139C VAL* 1.3 63.4 + - - +
140C GLU* 4.5 1.1 + - + -
155C ASN* 3.0 43.4 + - - -
156C ARG 4.7 0.9 - - - -
157C LEU* 3.4 35.3 - - + +
192C ALA* 3.7 8.7 - - - +
193C HIS* 3.4 62.4 + + + +
208C ASN* 6.0 0.2 - - - +
209C GLY* 4.6 4.4 - - - +
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Residues in contact with VAL 139 (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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137C GLN* 4.6 5.4 - - + +
138C HIS* 1.3 82.7 - - - +
140C GLU* 1.3 63.8 + - - +
141C LEU* 5.6 0.7 - - + -
155C ASN* 2.8 26.9 + - - -
156C ARG 3.5 20.8 + - - +
158C LEU* 3.6 29.4 - - + -
169C PHE* 5.1 12.5 - - + -
190C LEU* 3.6 42.8 - - + -
191C SER 3.8 5.4 - - - +
192C ALA* 6.1 0.2 - - + -
209C GLY* 6.3 1.1 - - - -
210C PHE* 5.7 4.5 - - + -
218C LEU* 6.0 4.7 - - + -
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Residues in contact with GLU 140 (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* 4.4 2.0 + - + -
139C VAL* 1.3 78.6 - - - +
141C LEU* 1.3 62.0 + - - +
142C TYR* 2.8 31.5 + - + -
152C TYR* 4.1 17.1 - - + -
154C SER 4.1 2.0 - - - -
155C ASN* 3.4 20.3 + - - +
190C LEU* 3.9 3.5 - - - -
191C SER* 3.3 31.7 + - - +
192C ALA 3.6 22.7 - - - +
193C HIS* 3.0 32.1 + - - -
194C CYS* 3.5 9.2 + - - +
140D GLU* 4.3 11.4 - - - +
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Residues in contact with LEU 141 (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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104C MET* 5.0 4.7 - - + -
126C LEU* 5.3 5.8 - - + -
139C VAL* 5.8 0.7 - - + -
140C GLU* 1.3 75.1 - - - +
142C TYR* 1.3 69.3 + - - +
152C TYR* 3.8 3.8 - - - -
153C LEU* 2.9 43.1 + - + -
154C SER* 3.2 34.5 + - - +
169C PHE* 4.1 31.2 - - + -
171C VAL* 4.3 12.6 - - + -
188C PHE* 4.9 9.0 - - + -
189C ARG 3.3 23.3 - - - +
190C LEU* 4.4 19.5 - - + -
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Residues in contact with TYR 142 (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* 2.8 36.5 + - + -
141C LEU* 1.3 75.5 - - - +
143C GLN* 1.3 60.8 + - - +
150C TRP* 3.8 28.3 - - + -
151C ARG 3.3 24.0 - - - +
152C TYR* 3.6 26.3 - + + -
153C LEU* 3.3 14.1 - - - +
188C PHE* 3.8 6.9 - - - -
189C ARG* 3.0 51.8 + - + +
191C SER* 3.1 28.3 - - - -
194C CYS* 4.6 9.1 - - - -
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Residues in contact with GLN 143 (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* 1.3 73.8 - - - +
144C LYS* 1.3 67.0 + - - +
145C TYR* 3.2 41.7 + - + -
150C TRP* 3.2 15.7 - - - -
151C ARG 2.9 25.6 + - - +
153C LEU* 3.6 28.9 - - + +
174C VAL* 3.5 23.2 - - + +
177C GLN* 5.1 5.5 + - - -
178C TRP* 3.2 41.6 - - + +
187C GLY 4.6 2.5 - - - -
188C PHE* 4.8 1.8 - - + -
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Residues in contact with LYS 144 (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* 6.0 0.9 - - - -
105C PHE* 3.2 34.4 - - + -
143C GLN* 1.3 81.0 + - - +
145C TYR* 1.3 69.4 + - - +
147C GLN* 3.5 48.3 - - - +
149C SER 5.1 0.2 - - - +
150C TRP* 3.5 22.6 - - + -
178C TRP* 4.9 0.3 + - - -
185C ILE* 3.4 30.2 + - - +
186C GLU* 3.9 18.6 - - - +
187C GLY 3.2 36.4 + - - +
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Residues in contact with TYR 145 (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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143C GLN* 3.2 51.4 + - + -
144C LYS* 1.3 77.8 - - - +
146C SER* 1.3 60.1 + - - +
147C GLN 2.9 7.8 + - - -
148C ASN 3.2 0.2 + - - -
149C SER* 2.7 53.3 + - - +
151C ARG* 3.5 37.7 - - + -
153C LEU* 5.8 0.2 - - + -
177C GLN* 4.8 7.3 + - - -
181C ARG* 6.1 3.1 - - - -
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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