Contacts of the helix formed by residues 148 - 168 (chain A) in PDB entry 1XFS
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A GLU 3.1 9.7 + - - -
146A GLU 3.3 1.6 + - - -
147A MSE 1.3 81.7 - - - +
149A PHE* 1.3 57.1 + - - +
150A HIS 3.5 1.3 - - - -
151A GLU* 4.1 11.9 - - - -
152A GLY* 2.7 35.6 + - - -
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Residues in contact with PHE 149 (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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12A LEU* 3.4 53.2 - - + -
13A MSE 4.3 14.6 - - - -
14A LEU* 4.8 7.0 - - + -
131A ALA 5.0 1.1 - - - -
133A ALA* 3.6 18.4 - - + -
144A HIS* 3.2 48.7 + + + +
145A GLU* 4.0 5.3 + - + -
147A MSE 3.6 0.2 - - - -
148A GLY* 1.3 76.1 - - - +
150A HIS* 1.3 80.0 + + + +
153A TRP* 2.8 83.2 + + + +
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Residues in contact with HIS 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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13A MSE 5.3 5.8 - - - -
14A LEU* 4.4 22.8 - - + +
145A GLU* 5.8 0.6 - - - +
149A PHE* 1.3 91.4 - + + +
151A GLU* 1.3 61.9 + - - +
153A TRP* 4.4 1.0 - - - +
154A GLY* 2.9 28.7 + - - -
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Residues in contact with GLU 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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148A GLY* 3.7 12.8 + - - +
149A PHE 3.4 0.2 - - - -
150A HIS* 1.3 83.7 + - - +
152A GLY* 1.3 59.5 + - - +
154A GLY* 3.3 1.3 + - - -
155A THR* 2.9 41.6 + - - +
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Residues in contact with GLY 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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41A PRO* 4.0 16.2 - - - +
148A GLY 2.7 23.5 + - - -
151A GLU* 1.3 75.6 - - - +
153A TRP* 1.3 64.2 + - - +
155A THR* 3.1 7.5 + - - -
156A THR* 3.1 27.3 + - - +
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Residues in contact with TRP 153 (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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14A LEU* 3.6 16.6 - - + -
88A TRP* 4.9 7.6 - + - -
114A MSE 3.9 26.5 - - + +
116A ALA* 4.1 23.1 - - + -
118A ILE* 4.4 8.5 - - + -
129A TYR* 4.4 5.2 - - - -
131A ALA* 3.7 34.1 - - + -
132A CYS 5.1 0.4 - - - -
133A ALA* 4.4 6.5 - - + -
144A HIS* 4.1 8.5 + - - -
149A PHE* 2.8 65.1 + + + +
152A GLY* 1.3 73.2 - - - -
154A GLY* 1.3 61.4 + - - +
156A THR* 2.7 29.7 + - + -
157A ILE* 3.1 14.5 + - + +
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Residues in contact with GLY 154 (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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14A LEU* 3.6 11.8 - - - +
16A ARG* 2.9 31.7 + - - -
150A HIS* 2.9 20.6 + - - -
151A GLU* 3.7 1.6 - - - -
153A TRP* 1.3 78.3 - - - +
155A THR* 1.3 60.4 + - - +
157A ILE 3.4 0.2 + - - -
158A THR* 3.2 12.8 + - - -
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Residues in contact with THR 155 (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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41A PRO* 3.7 16.4 - - + -
42A LYS 4.9 2.7 - - - +
151A GLU* 2.9 27.7 + - - +
152A GLY 3.1 5.4 + - - -
154A GLY* 1.3 75.0 - - - +
156A THR* 1.3 65.6 + - - +
158A THR* 3.2 9.5 + - - -
159A GLN* 3.0 42.5 + - + +
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Residues in contact with THR 156 (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 TRP* 3.3 34.4 - - - +
39A PHE 3.4 21.5 - - - +
41A PRO* 3.5 23.8 - - + -
152A GLY 3.1 15.7 + - - +
153A TRP* 2.7 26.3 + - + +
155A THR* 1.3 75.6 - - - +
157A ILE* 1.3 63.8 + - - +
159A GLN* 3.2 5.4 + - - +
160A LEU 2.9 23.4 + - - -
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Residues in contact with ILE 157 (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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14A LEU* 4.2 12.3 - - + -
16A ARG* 3.7 39.9 - - + +
18A LEU* 4.1 22.2 - - + +
38A TRP* 4.4 10.3 - - + -
129A TYR* 3.3 46.9 - - + +
153A TRP* 3.1 15.2 + - + +
155A THR 3.2 0.2 - - - -
156A THR* 1.3 83.3 + - - +
158A THR* 1.3 63.3 + - - +
160A LEU* 3.2 7.4 + - + +
161A GLU* 3.0 22.7 + - - +
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Residues in contact with THR 158 (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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16A ARG* 2.9 25.5 + - - +
154A GLY 3.2 8.5 + - - -
155A THR* 3.2 12.7 + - - -
157A ILE* 1.3 79.6 - - - +
159A GLN* 1.3 63.4 + - + +
161A GLU* 3.4 7.1 + - - +
162A GLU* 3.1 24.5 + - + +
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Residues in contact with GLN 159 (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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37A LYS 4.6 4.9 + - - +
38A TRP* 3.0 28.0 + - + +
40A VAL 2.9 25.8 + - - -
41A PRO* 3.9 0.2 - - - +
42A LYS* 3.1 44.3 + - + +
155A THR* 3.0 32.9 + - + +
156A THR* 3.5 5.9 - - - +
158A THR* 1.3 77.8 - - + +
160A LEU* 1.3 57.8 + - - +
162A GLU* 3.4 15.8 + - - +
163A LEU* 3.0 29.8 + - - +
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Residues in contact with LEU 160 (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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18A LEU* 4.2 16.4 - - + -
25A VAL* 4.6 15.3 - - + +
28A GLY* 4.1 10.8 - - - -
29A LEU* 4.7 7.6 - - + -
38A TRP* 3.6 56.0 - - + +
129A TYR* 5.1 3.4 - - + -
156A THR 2.9 14.0 + - - +
157A ILE* 3.4 17.3 - - + +
159A GLN* 1.3 73.2 - - - +
161A GLU* 1.3 67.0 + - - +
163A LEU* 3.1 5.7 + - + +
164A LEU* 3.0 50.9 + - + +
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Residues in contact with GLU 161 (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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16A ARG* 4.7 11.8 + - - -
17A GLU 4.2 7.3 - - - +
18A LEU* 3.6 30.0 - - + +
19A ALA* 2.9 27.0 + - - +
20A VAL* 4.3 4.7 - - + -
157A ILE* 3.0 15.0 + - + +
158A THR* 3.9 5.5 - - - +
160A LEU* 1.3 77.0 - - - +
162A GLU* 1.3 62.4 + - - +
164A LEU* 3.6 5.1 + - - +
165A LYS* 3.2 60.5 + - - +
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Residues in contact with GLU 162 (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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42A LYS* 5.1 9.0 + - - -
158A THR* 3.1 20.0 + - + +
159A GLN* 3.6 13.3 - - - +
160A LEU 3.2 0.2 - - - -
161A GLU* 1.3 78.7 - - - +
163A LEU* 1.3 61.3 + - - +
165A LYS* 3.6 7.1 + - - +
166A GLN* 3.5 28.3 + - + +
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Residues in contact with LEU 163 (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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34A LEU* 3.6 49.6 - - + +
37A LYS* 4.0 33.9 - - + +
38A TRP* 3.8 16.2 - - + -
159A GLN 3.0 17.5 + - - +
160A LEU* 3.1 7.6 + - + +
162A GLU* 1.3 77.6 - - - +
164A LEU* 1.3 61.0 + - + +
166A GLN* 3.3 4.2 + - + +
167A GLU* 3.0 39.7 + - + +
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Residues in contact with LEU 164 (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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18A LEU* 5.2 0.9 - - + -
20A VAL* 4.0 24.7 - - + -
24A LEU* 3.7 25.4 - - + +
25A VAL* 3.6 34.8 - - + +
27A ARG* 5.8 0.2 - - + -
28A GLY* 4.3 12.8 - - - +
34A LEU* 4.6 12.6 - - + -
160A LEU* 3.0 35.0 + - + +
161A GLU* 4.1 4.7 - - - +
163A LEU* 1.3 82.6 - - + +
165A LYS* 1.3 57.7 + - - +
167A GLU* 4.8 3.6 - - + -
168A LYS* 2.9 33.4 + - - +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.0 23.2 - - - +
20A VAL* 4.0 11.0 - - + -
161A GLU* 3.2 53.5 + - + +
162A GLU* 3.9 7.6 - - - +
163A LEU 3.2 0.4 - - - -
164A LEU* 1.3 78.1 - - - +
166A GLN* 1.3 74.0 + - - +
168A LYS* 3.5 20.8 - - + +
169A ALA 5.0 0.2 + - - -
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Residues in contact with GLN 166 (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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162A GLU* 3.5 20.8 + - + +
163A LEU* 3.3 5.1 + - - +
165A LYS* 1.3 90.3 + - - +
167A GLU* 1.3 61.4 + - - +
168A LYS 3.3 2.9 + - - -
169A ALA* 4.7 5.8 + - - +
170A TYR* 5.4 0.3 + - - +
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Residues in contact with GLU 167 (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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34A LEU* 4.6 19.2 - - + +
37A LYS* 4.9 9.9 + - - -
163A LEU* 3.0 27.7 + - + +
164A LEU* 3.8 4.3 - - + +
166A GLN* 1.3 77.0 - - - +
168A LYS* 1.3 66.2 + - - +
169A ALA 3.3 2.7 - - - -
170A TYR* 3.1 48.3 + - + +
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Residues in contact with LYS 168 (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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20A VAL* 5.9 2.9 - - + +
21A PRO* 4.4 15.7 - - + -
24A LEU* 3.7 35.9 - - + +
164A LEU 2.9 18.2 + - - +
165A LYS* 3.5 17.9 - - + +
166A GLN 3.3 1.0 - - - -
167A GLU* 1.3 79.2 - - - +
169A ALA* 1.3 65.9 + - - +
170A TYR 4.0 3.5 - - - -
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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