Contacts of the helix formed by residues 125 - 140 (chain D) in PDB entry 1F5Q
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 125 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA* 3.5 9.6 - - - -
123D ALA 3.6 11.2 + - - +
124D THR* 1.3 81.3 - - - +
126D ALA* 1.3 64.6 + - - +
127D ASP* 3.6 11.9 + - - +
128D LYS* 3.0 40.4 + - + +
129D LEU* 3.1 13.0 + - - +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR 5.8 0.7 - - - +
113D ALA* 3.5 27.8 - - + -
114D THR* 3.5 27.6 - - + +
117D ALA* 3.5 8.8 - - - +
125D THR* 1.3 73.5 - - - +
127D ASP* 1.3 59.8 + - - +
129D LEU* 3.8 3.2 - - - +
130D LEU* 2.8 41.3 + - + +
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLN* 5.2 0.3 + - - -
212B GLU* 3.8 28.9 - - + +
216B ASP* 5.0 7.4 - - - +
125D THR* 3.0 11.2 - - - +
126D ALA* 1.3 77.5 - - - +
128D LYS* 1.3 61.9 + - + +
130D LEU* 3.3 11.5 + - - +
131D THR* 2.9 31.5 + - - -
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ASP* 5.0 11.5 + - - +
212B GLU* 3.9 14.3 + - - +
213B ASN* 4.1 25.5 + - - +
93D SER* 5.9 2.0 - - - +
123D ALA* 3.8 29.4 - - - +
124D THR* 4.4 5.8 - - + -
125D THR* 3.0 23.8 + - - +
127D ASP* 1.3 76.8 - - + +
129D LEU* 1.3 60.2 + - + +
131D THR* 3.1 4.8 + - - -
132D LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D SER* 3.7 44.2 - - - +
96D ALA* 4.0 17.9 - - + -
97D VAL* 3.4 12.4 - - + +
100D HIS* 5.7 5.6 + - + +
113D ALA* 3.9 13.5 - - + +
116D LEU* 4.1 5.2 - - + -
117D ALA* 3.6 38.4 - - + +
120D CYS* 5.1 0.2 - - - -
124D THR* 3.7 12.8 - - + -
125D THR 3.1 10.7 + - - +
126D ALA* 3.9 6.1 - - - +
128D LYS* 1.3 76.5 - - + +
130D LEU* 1.3 57.9 + - - +
132D LEU* 3.2 6.4 + - + +
133D GLU* 2.8 27.3 + - - +
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLN* 3.8 12.2 + - - +
40C GLU 5.1 1.6 - - - +
41C THR 3.3 22.4 - - - +
42C GLU* 3.7 28.3 - - - +
43C GLY* 3.8 9.6 - - - +
100D HIS* 3.9 12.6 - - + -
113D ALA* 4.5 6.7 - - + -
126D ALA* 2.8 33.2 + - + +
127D ASP* 3.7 11.7 - - - +
128D LYS 3.2 0.2 - - - -
129D LEU* 1.3 73.7 - - - +
131D THR* 1.3 63.6 + - - +
133D GLU* 3.5 18.3 + - - +
134D VAL* 3.3 27.0 + - - +
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLN* 4.0 33.0 + - - +
207B LYS 6.2 0.2 - - - -
209B ASP* 5.4 4.5 - - - +
212B GLU* 2.3 39.2 + - - +
127D ASP 2.9 10.1 + - - -
128D LYS* 3.6 7.6 - - - -
130D LEU* 1.3 73.7 - - - +
132D LEU* 1.3 67.1 + - - +
134D VAL* 3.4 4.6 + - - +
135D LYS* 3.3 48.5 + - - +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ASN* 4.9 8.5 - - + +
93D SER* 3.6 36.3 - - - -
94D THR* 4.0 15.5 - - + +
97D VAL* 3.5 15.9 - - + -
128D LYS 2.9 13.4 + - - +
129D LEU* 3.3 11.0 - - + +
131D THR* 1.3 78.8 - - - +
133D GLU* 1.3 56.4 + - - +
135D LYS* 3.3 12.4 + - + +
136D SER* 2.8 42.0 + - - +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 4.1 9.2 + - - +
97D VAL* 3.6 16.1 - - + +
100D HIS* 2.5 34.6 + - - +
101D ILE* 3.6 27.2 + - + +
104D LYS* 2.7 31.9 + - - +
129D LEU 2.8 16.5 + - - +
130D LEU* 3.6 17.1 - - - +
131D THR 3.3 0.2 - - - -
132D LEU* 1.3 76.7 - - - +
134D VAL* 1.3 53.6 + - - +
136D SER* 3.1 2.3 + - - -
137D LEU* 2.7 50.7 + - + +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLN* 3.6 31.2 - - + +
37C LEU* 5.1 8.1 - - + +
44C VAL* 4.8 15.5 - - + -
71C HIS* 3.4 34.5 - - + +
130D LEU 3.3 15.0 + - - +
131D THR* 3.7 7.6 - - - +
132D LEU 3.3 0.6 - - - -
133D GLU* 1.3 77.8 - - + +
135D LYS* 1.3 65.8 + - + +
137D LEU* 3.2 7.2 + - - +
138D ASP* 2.9 24.5 + - - +
142D TRP* 3.9 10.4 - - + -
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLN 3.9 14.6 - - - +
207B LYS* 4.7 12.2 + - - +
209B ASP* 4.7 11.3 + - - -
131D THR* 3.3 36.5 - - + +
132D LEU* 3.3 14.7 + - + +
134D VAL* 1.3 78.8 - - + +
136D SER* 1.3 61.0 + - - +
138D ASP* 3.2 14.0 - - - +
139D THR* 3.0 25.4 + - - -
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.9 25.1 - - - +
94D THR* 5.4 3.5 - - - +
97D VAL* 3.8 19.6 - - - +
101D ILE* 4.4 4.3 - - - -
132D LEU* 2.8 34.8 + - - +
133D GLU 3.4 4.3 - - - -
135D LYS* 1.3 78.3 - - - +
137D LEU* 1.3 57.6 + - - +
139D THR* 3.2 9.8 + - - -
140D LEU* 3.0 31.9 + - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.9 13.2 - - + -
49C ILE* 4.2 16.2 - - + -
101D ILE* 3.9 29.4 - - + -
104D LYS* 6.1 1.6 - - + -
133D GLU* 2.7 39.5 + - + +
134D VAL 3.6 4.5 - - - +
136D SER* 1.3 70.8 - - - +
138D ASP* 1.3 60.0 + - - +
140D LEU* 3.1 9.3 + - + -
141D SER 2.9 8.0 + - - -
142D TRP* 2.8 72.4 + - + -
144D ALA* 4.3 14.8 - - + -
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C HIS* 3.0 38.4 + - - +
134D VAL* 2.9 14.8 + - - +
135D LYS* 3.2 17.0 - - - +
137D LEU* 1.3 76.1 - - - +
139D THR* 1.3 63.8 + - - +
141D SER* 3.0 15.2 + - - -
142D TRP* 3.1 14.7 + - - +
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Residues in contact with THR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU* 5.5 3.1 - - + +
80D LEU* 4.2 11.1 - - + +
83D SER* 3.7 16.8 - - - +
84D THR* 3.5 32.2 - - + +
135D LYS 3.0 14.6 + - - -
136D SER* 3.3 9.4 - - - -
138D ASP* 1.3 80.9 - - - +
140D LEU* 1.3 59.3 + - + +
141D SER* 3.2 7.5 + - - -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 3.8 34.3 - - + -
79D GLU* 4.2 20.4 - - + +
80D LEU* 4.2 22.9 - - + -
101D ILE* 4.5 6.5 - - + -
136D SER 3.0 16.9 + - - +
137D LEU* 3.1 24.4 + - + +
139D THR* 1.3 75.8 - - + +
141D SER* 1.3 70.7 + - - +
142D TRP 3.1 2.7 + - - +
143D VAL* 3.2 28.2 + - - +
144D ALA* 4.9 1.8 - - + -
146D ARG* 4.1 18.4 + - - +
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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
------------------------------------------------------------
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