Contacts of the strand formed by residues 137 - 143 (chain F) in PDB entry 1FPY
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 ASP 137 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E TYR 4.9 2.4 + - - -
167E GLY* 3.6 13.2 - - - -
168E ASN* 2.7 36.3 + - - +
135F PHE* 3.6 4.0 - - - +
136F ASP* 1.3 84.9 - - + +
138F ILE* 1.3 61.5 + - - +
139F ARG* 2.6 35.4 + - - +
150F ALA 4.6 1.4 - - - +
151F ILE* 3.7 1.4 - - - -
152F ASP* 2.9 48.6 + - + +
252F THR* 4.7 0.4 - - - -
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER 3.9 1.9 - - - +
168E ASN* 2.9 37.7 + - - +
169E LYS 4.0 1.8 - - - -
170E GLY* 3.8 19.7 - - - +
135F PHE* 5.0 3.4 - - + -
137F ASP* 1.3 76.3 - - - +
139F ARG* 1.3 68.7 + - - +
140F PHE* 4.0 12.9 - - + -
149F VAL* 4.3 9.0 - - + -
150F ALA 3.4 15.7 - - - +
151F ILE* 4.0 21.8 - - + -
252F THR* 4.0 3.4 - - + +
462L PHE* 4.4 8.5 - - + -
466L TYR* 3.6 49.8 - - + +
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Residues in contact with ARG 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER 3.2 8.1 - - - +
161E SER* 3.5 15.4 + - - +
162E THR 3.5 20.0 - - - +
163E LYS* 3.4 44.1 - - - +
168E ASN* 3.8 7.0 - - + +
137F ASP* 2.6 41.2 + - - +
138F ILE* 1.3 81.0 - - - +
140F PHE* 1.3 66.0 + - - +
148F HIS* 4.4 6.6 + - - +
149F VAL* 3.2 2.5 - - - +
150F ALA* 2.6 62.1 + - + +
152F ASP* 5.8 0.6 - - - +
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Residues in contact with PHE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER* 3.0 56.1 + - - -
161E SER* 3.3 2.8 + - - -
170E GLY* 4.9 14.8 - - - -
138F ILE* 4.0 22.0 - - + -
139F ARG* 1.3 80.6 - - - +
141F GLY* 1.3 62.6 + - - +
148F HIS* 3.0 27.5 + - - +
149F VAL* 3.9 9.6 - - + -
459L PRO 4.5 3.1 - - - +
462L PHE* 3.6 34.5 - - + -
463L GLU* 3.4 36.3 - - + -
466L TYR* 4.5 9.6 - + + -
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Residues in contact with GLY 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER* 4.5 4.0 - - - -
161E SER* 4.9 2.7 - - - -
140F PHE* 1.3 84.0 - - - +
142F ALA* 1.3 59.9 + - - -
147F SER* 3.0 5.5 - - - -
148F HIS* 2.8 44.8 + - - +
459L PRO* 4.3 3.7 + - - +
463L GLU* 4.7 4.3 - - - -
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F GLY* 1.3 75.6 - - - +
143F SER* 1.3 62.5 + - - +
146F GLY 3.5 6.3 - - - +
147F SER* 3.8 12.6 - - - -
452F ARG* 4.6 7.5 + - - +
456F THR* 4.8 6.3 - - + +
460L VAL* 4.1 18.6 - - + -
463L GLU* 4.0 19.0 + - - +
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Residues in contact with SER 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 1.3 77.8 - - - +
144F ILE* 1.3 70.0 + - - +
145F SER* 3.0 23.1 + - - -
146F GLY 2.7 20.7 + - - +
158L TRP* 6.0 0.3 - - - +
261L PHE* 5.5 8.0 - - - +
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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