Contacts of the helix formed by residues 138 - 146 (chain A) in PDB entry 1F3Y
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 THR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.8 27.4 - - + +
28A ILE* 3.7 0.9 - - - -
137A VAL* 1.3 78.3 - - - +
139A PRO* 1.3 66.6 - - - +
140A GLU* 3.8 4.4 + - - +
141A GLN* 2.8 42.2 + - + +
142A LEU* 2.6 34.8 + - - +
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Residues in contact with PRO 139 (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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26A LYS 3.5 18.2 - - - +
28A ILE* 3.2 26.6 - - + -
138A THR* 1.3 89.9 - - + +
140A GLU* 1.3 63.5 + - - +
142A LEU* 3.2 2.8 + - - +
143A ILE* 3.1 26.5 + - - +
158A LEU* 3.2 31.8 - - + +
165A LEU* 3.5 22.7 - - + -
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Residues in contact with GLU 140 (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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138A THR* 3.4 3.8 - - - +
139A PRO* 1.3 80.8 - - - +
141A GLN* 1.3 61.2 + - + +
143A ILE* 3.6 4.7 + - - +
144A ASP* 3.3 20.1 + - - +
155A LYS* 3.3 30.6 + - - +
158A LEU* 3.8 2.0 - - + +
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Residues in contact with GLN 141 (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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27A LYS* 4.6 8.1 - - - +
137A VAL* 3.9 14.6 - - + +
138A THR* 2.8 48.6 + - + +
140A GLU* 1.3 76.2 - - + +
142A LEU* 1.3 60.8 + - - +
143A ILE 3.1 0.2 - - - -
144A ASP* 2.9 23.8 + - + +
145A LEU* 2.9 30.7 + - + +
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Residues in contact with LEU 142 (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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28A ILE* 3.9 15.9 - - + -
29A PHE 4.1 5.2 - - - +
30A ALA* 3.1 43.7 - - + +
40A TRP* 4.8 1.1 - - + -
41A GLN* 4.3 13.7 - - - +
42A MET* 3.7 30.3 - - + -
137A VAL* 3.4 13.6 - - + +
138A THR 2.6 20.0 + - - +
139A PRO 3.6 4.5 - - - +
141A GLN* 1.3 72.0 - - - +
143A ILE* 1.3 54.8 + - + +
145A LEU* 4.2 2.9 - - - +
146A THR* 2.6 39.8 + - - -
154A TYR* 3.7 22.2 - - + -
158A LEU* 5.7 2.2 - - + -
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Residues in contact with ILE 143 (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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139A PRO 3.1 16.7 + - - +
140A GLU 3.7 2.2 - - - +
141A GLN 3.1 0.2 - - - -
142A LEU* 1.3 78.4 - - + +
144A ASP* 1.3 61.8 + - - +
146A THR* 3.0 19.7 - - - +
151A LYS* 3.0 41.0 - - + +
154A TYR* 3.0 40.8 - - + -
155A LYS* 3.1 45.1 - - + +
158A LEU* 3.3 15.9 - - + -
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Residues in contact with ASP 144 (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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140A GLU 3.3 10.9 + - - +
141A GLN* 2.9 12.9 + - + +
143A ILE* 1.3 82.6 - - - +
145A LEU* 1.3 65.6 + - + +
146A THR 3.4 6.4 + - - +
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Residues in contact with LEU 145 (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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38A ASP 2.6 29.0 - - - +
40A TRP* 3.1 45.3 + - + +
137A VAL* 4.5 19.3 - - + -
141A GLN* 2.9 44.3 + - + +
142A LEU* 4.2 3.1 - - - +
144A ASP* 1.3 76.9 - - + +
146A THR* 1.3 62.3 + - - +
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Residues in contact with THR 146 (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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38A ASP 4.6 1.7 - - - +
40A TRP* 2.4 27.1 + - - +
41A GLN* 3.9 1.0 - - - +
142A LEU* 2.6 22.6 + - - +
143A ILE* 3.0 32.8 - - - +
144A ASP 3.5 7.8 - - - +
145A LEU* 1.3 77.6 - - - +
147A VAL* 1.3 69.4 + - - +
148A GLU 3.9 0.5 + - - -
150A LYS* 4.0 2.9 - - - +
151A LYS* 3.8 22.1 - - + +
154A TYR* 3.4 26.3 - - + -
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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