Contacts of the strand formed by residues 146 - 152 (chain F) in PDB entry 1F1H
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 GLY 146 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 3.4 1.4 - - - +
143F SER* 2.8 40.0 + - - +
144F ILE 3.4 1.6 + - - -
145F SER* 1.3 81.8 + - - +
147F SER* 1.3 63.3 + - - -
456F THR* 6.1 0.2 - - - +
149L VAL* 3.2 19.5 - - - -
150L ALA* 4.7 0.4 - - - -
151L ILE* 5.5 1.1 - - - -
259L PRO 6.1 0.9 - - - -
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Residues in contact with SER 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F GLY 3.2 13.7 - - - -
142F ALA* 4.2 8.7 - - - -
146F GLY* 1.3 77.0 - - - -
148F HIS* 1.3 69.7 + - - +
456F THR* 4.6 6.4 - - - +
457F PRO 3.5 21.0 + - - -
459F PRO* 4.2 3.2 - - - +
148L HIS* 3.3 0.7 - - - -
149L VAL* 2.9 40.6 + - - +
458L HIS* 5.1 0.7 - - - -
459L PRO* 3.7 20.2 - - - -
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Residues in contact with HIS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E SER* 3.5 37.3 + - - -
139F ARG* 4.3 11.3 + - + +
140F PHE* 3.1 15.8 + - - +
141F GLY* 2.9 47.5 + - - +
147F SER* 1.3 80.6 - - - +
149F VAL* 1.3 67.8 + - - +
150F ALA* 4.6 5.2 - - + -
147L SER 3.3 7.4 - - - -
148L HIS* 3.4 19.5 - - + -
459L PRO* 3.6 10.2 - - - +
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ILE* 4.3 7.0 - - + -
139F ARG 3.2 10.3 - - - +
140F PHE* 4.1 3.6 - - + -
148F HIS* 1.3 76.2 - - - +
150F ALA* 1.3 67.8 + - - +
151F ILE* 4.5 4.5 - - + -
146L GLY* 3.2 8.4 - - - -
147L SER* 2.9 49.1 + - - +
457L PRO* 5.0 1.6 - - + +
459L PRO* 4.2 9.2 - - + -
462L PHE* 3.7 55.2 - - + -
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Residues in contact with ALA 150 (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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137F ASP 3.9 1.4 - - - +
138F ILE* 3.6 4.5 - - - +
139F ARG* 2.7 69.1 + - + +
148F HIS* 5.0 5.2 - - + -
149F VAL* 1.3 74.3 - - - +
151F ILE* 1.3 63.1 + - - +
145L SER 3.8 3.4 - - - -
146L GLY* 4.7 0.2 - - - -
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Residues in contact with ILE 151 (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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135F PHE* 3.6 36.1 - - + -
137F ASP 3.8 2.9 - - - -
138F ILE* 3.8 20.4 - - + -
149F VAL* 4.5 5.6 - - + -
150F ALA* 1.3 73.7 - - - +
152F ASP* 1.3 70.5 + - - +
158F TRP* 3.7 15.6 + - + -
259F PRO* 3.5 36.1 - - + +
260F MET* 3.7 17.7 - - + -
145L SER* 2.8 38.4 + - - +
146L GLY* 5.6 0.7 - - - -
462L PHE* 4.3 6.5 - - + -
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Residues in contact with ASP 152 (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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135F PHE* 3.6 1.9 - - - +
136F ASP* 2.9 24.3 + - + -
137F ASP* 2.9 37.8 + - + +
139F ARG* 5.5 2.5 - - - +
151F ILE* 1.3 81.5 - - - +
153F ASP* 1.3 61.3 + - - +
158F TRP* 2.9 25.8 + - - -
159F ASN* 2.9 22.0 + - - +
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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