Contacts of the strand formed by residues 137 - 143 (chain L) in PDB entry 5FHX
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 137 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129L LEU* 3.7 26.0 - - + -
130L SER 5.3 1.1 - - - +
131L VAL* 3.5 22.9 - - + -
135L ASP* 4.1 18.8 - - + +
136L THR* 1.3 82.5 - - - +
138L THR* 1.3 70.8 + - - +
139L LEU* 3.8 26.0 - - + -
191L LEU 4.3 0.2 - - - -
192L THR* 3.1 4.7 - - - +
193L ILE* 2.8 47.8 + - + +
196L LEU* 5.3 3.6 - - + -
222L LEU* 4.5 11.2 - - + -
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Residues in contact with THR 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L PRO* 5.0 5.2 - - - +
129L LEU* 5.5 3.0 - - - +
136L THR* 5.2 2.3 - - - +
137L ILE* 1.3 75.6 + - - +
139L LEU* 1.3 65.5 + - - +
140L THR* 5.1 3.4 + - - +
190L THR* 4.1 24.5 - - + -
191L LEU 3.2 6.3 - - - +
192L THR* 2.8 28.6 + - - +
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Residues in contact with LEU 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L SER 4.0 4.0 - - - +
126L PRO* 4.6 3.1 - - + -
129L LEU* 4.4 7.4 - - + -
137L ILE* 3.8 24.9 - - + -
138L THR* 1.3 75.9 - - - +
140L THR* 1.3 61.6 + - - +
153L TRP* 4.3 12.2 - - + -
190L THR* 3.2 8.5 - - - -
191L LEU* 2.8 47.1 + - + +
193L ILE* 5.0 3.6 - - + -
204L TYR* 3.8 38.6 - - + -
220L THR* 3.8 38.1 - - + +
222L LEU* 4.2 8.7 - - + -
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Residues in contact with THR 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L THR 5.4 0.7 - - - +
124L GLN* 3.3 8.5 + - - +
125L SER* 3.0 53.2 + - - +
138L THR* 4.3 4.2 + - - +
139L LEU* 1.3 74.9 + - - +
141L CYS* 1.3 71.5 + - - +
142L HIS* 4.9 4.9 - - + +
153L TRP* 4.4 2.3 - - - -
188L GLY* 6.5 0.2 - - - -
189L PHE 3.5 5.4 - - - +
190L THR* 4.0 12.9 - - + +
220L THR* 4.9 0.2 + - - -
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Residues in contact with CYS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L MET* 3.6 18.6 - - - -
123L THR 3.4 6.7 - - - -
124L GLN* 4.2 1.1 - - + -
140L THR* 1.3 78.4 - - - +
142L HIS* 1.3 63.5 + - - +
151L LEU* 3.7 11.0 - - - -
153L TRP* 3.7 20.4 - - + -
187L THR 3.7 0.5 - - - +
188L GLY* 3.8 0.7 - - - -
189L PHE* 2.8 39.4 + - + +
206L CYS* 2.6 44.0 - - - -
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Residues in contact with HIS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L GLN 3.6 1.9 - - - +
122L MET* 3.5 10.5 - - - +
123L THR* 2.8 49.3 + - + +
140L THR* 5.4 6.1 - - + -
141L CYS* 1.3 75.3 - - - +
143L ALA* 1.4 78.8 + - - +
144L SER* 4.3 7.7 + - - -
187L THR* 3.2 27.0 + - - -
188L GLY* 4.7 4.0 - - - -
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Residues in contact with ALA 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L ILE* 4.2 1.1 - - + -
121L GLN 3.7 4.3 - - - -
122L MET* 4.0 14.6 - - + +
142L HIS* 1.4 86.7 - - - +
144L SER* 1.3 58.1 + - - +
145L GLN 3.0 26.2 + - - +
147L ILE* 3.9 26.2 - - + -
187L THR* 2.8 30.8 + - - +
189L PHE* 4.8 0.6 - - + -
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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