Contacts of the strand formed by residues 146 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ALA* 3.4 1.6 - - - +
143A SER* 2.8 38.2 + - - +
144A ILE 3.4 1.8 + - - -
145A SER* 1.3 80.7 + - - +
147A SER* 1.3 63.0 + - - -
456A THR* 6.1 0.3 - - - +
149G VAL* 3.3 19.3 - - - -
150G ALA* 4.8 0.4 - - - -
151G ILE* 5.6 1.1 - - - -
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY 3.2 13.7 - - - -
142A ALA* 4.2 8.7 - - - -
146A GLY* 1.3 75.4 - - - -
148A HIS* 1.3 69.7 + - - +
456A THR* 4.6 6.2 - - - +
457A PRO 3.5 20.7 + - - -
459A PRO* 4.2 2.9 - - - +
148G HIS* 3.4 0.3 - - - -
149G VAL* 3.0 39.8 + - - +
458G HIS* 5.2 0.9 - - - -
459G PRO* 3.7 20.2 - - - -
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Residues in contact with HIS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 4.3 11.3 + - + +
140A PHE* 3.1 15.1 + - - +
141A GLY* 2.9 46.8 + - - +
147A SER* 1.3 80.8 - - - +
149A VAL* 1.3 68.3 + - - +
150A ALA* 4.6 4.9 - - + -
161F SER* 3.4 38.5 + - - -
147G SER 3.4 7.4 - - - -
148G HIS* 3.5 18.4 - - + -
459G PRO* 3.6 10.2 - - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 4.3 7.0 - - + -
139A ARG 3.2 12.1 - - - +
140A PHE* 4.0 3.6 - - + -
148A HIS* 1.3 75.6 - - - +
150A ALA* 1.3 67.0 + - - +
151A ILE* 4.2 5.2 - - + -
146G GLY* 3.3 8.0 - - - -
147G SER* 3.0 44.9 + - - +
457G PRO* 5.1 0.9 - - + +
459G PRO* 4.2 9.6 - - + -
462G PHE* 3.6 56.1 - - + -
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP 3.9 1.2 - - - +
138A ILE* 3.6 4.2 - - - +
139A ARG* 2.7 69.6 + - + +
148A HIS* 4.6 5.6 - - + -
149A VAL* 1.3 74.5 - - - +
151A ILE* 1.3 63.2 + - - +
145G SER 3.8 3.1 - - - -
146G GLY* 4.8 0.4 - - - -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.6 36.1 - - + -
137A ASP 3.8 2.7 - - - -
138A ILE* 3.8 21.1 - - + -
149A VAL* 4.5 5.2 - - + -
150A ALA* 1.3 74.5 - - - +
152A ASP* 1.3 71.0 + - - +
158A TRP* 3.7 23.3 + - + -
259A PRO* 3.5 35.7 - - + +
260A MET* 3.7 18.2 - - + -
145G SER* 2.9 29.9 + - - +
146G GLY* 5.6 0.9 - - - -
462G PHE* 4.2 7.4 - - + -
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.6 1.9 - - - +
136A ASP* 2.9 23.8 + - - -
137A ASP* 2.9 39.7 + - + +
139A ARG* 5.5 1.6 - - - +
151A ILE* 1.3 79.8 - - - +
153A ASP* 1.3 61.8 + - - +
158A TRP* 2.9 25.3 + - - -
159A 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