Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 1XSC
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 PHE 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ILE* 4.0 20.4 - - + -
42A HIS* 3.3 32.5 - + + -
44A THR* 5.6 2.5 - - + -
131A ALA* 2.6 21.8 + - - +
132A GLN* 1.3 80.9 - - + +
134A LYS* 1.3 67.4 + - - +
135A GLU* 3.2 11.9 - - - +
136A MET* 2.9 22.3 + - + +
137A LYS* 3.0 3.3 + - - +
154A ATP 3.0 75.4 - + - +
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Residues in contact with LYS 134 (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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132A GLN 3.0 8.5 + - - -
133A PHE* 1.3 69.2 - - - +
135A GLU* 1.3 79.1 + - + +
137A LYS* 2.9 21.3 + - - +
138A ALA* 2.9 31.8 + - + +
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Residues in contact with GLU 135 (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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85A LEU* 3.1 38.8 - - + +
86A ASN 5.7 1.6 - - - +
87A TYR* 3.9 12.3 - - + +
133A PHE* 3.2 17.5 - - - +
134A LYS* 1.3 87.7 + - + +
136A MET* 1.3 59.9 + - - +
138A ALA* 3.4 6.7 + - - +
139A ALA* 3.1 15.9 + - - +
154A ATP 2.5 43.3 + - - +
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Residues in contact with MET 136 (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 ILE* 5.0 0.9 - - + -
44A THR* 3.5 31.4 - - + -
45A PRO* 3.5 17.7 - - + -
85A LEU* 4.3 5.4 - - + -
87A TYR* 5.8 2.0 - - - -
98A TYR* 2.9 51.1 - - + +
131A ALA* 3.5 18.6 - - + +
133A PHE* 2.9 20.3 + - + +
135A GLU* 1.3 71.6 - - - +
137A LYS* 1.3 65.6 + - - +
138A ALA 2.9 4.9 - - - -
139A ALA* 2.9 23.0 + - + +
140A LEU* 2.9 26.1 + - + +
154A ATP 4.5 5.6 - - - +
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Residues in contact with LYS 137 (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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128A CYS* 3.2 51.0 - - + +
131A ALA 2.8 24.4 + - - +
132A GLN* 2.9 24.7 - - - +
133A PHE 3.0 6.4 + - - +
134A LYS* 2.9 19.6 + - + +
136A MET* 1.3 76.3 - - - +
138A ALA* 1.3 56.3 + - - +
140A LEU* 3.9 1.8 - - - -
141A GLN* 2.9 33.8 + - + +
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Residues in contact with ALA 138 (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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85A LEU* 6.1 0.9 - - + -
134A LYS* 2.9 20.6 + - + +
135A GLU* 3.5 11.4 - - - +
136A MET 2.9 0.6 - - - -
137A LYS* 1.3 76.5 - - - +
139A ALA* 1.3 57.1 + - - +
141A GLN* 2.8 10.0 + - - +
142A GLU* 2.6 51.7 + - + +
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Residues in contact with ALA 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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14A ILE* 3.1 33.2 - - + +
81A PHE* 3.9 6.3 - - - -
83A ARG* 5.9 2.7 - - + -
85A LEU* 4.7 5.1 - - + +
98A TYR* 3.4 24.0 - - + -
135A GLU 3.1 8.8 + - - +
136A MET* 2.9 16.5 + - + +
138A ALA* 1.3 76.4 - - - +
140A LEU* 1.3 59.5 + - - +
142A GLU* 3.4 8.7 + - - -
143A GLY* 3.1 20.8 + - - -
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Residues in contact with LEU 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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14A ILE* 4.3 18.6 - - + -
31A PHE* 3.7 30.9 - - + -
32A LEU 5.4 2.0 - - - +
33A LEU* 5.0 11.2 - - + -
45A PRO* 5.4 4.0 - - + -
124A LEU* 3.4 23.1 - - + +
127A ALA* 3.6 41.5 - - + +
128A CYS 4.4 0.4 - - - +
131A ALA* 3.9 7.4 - - + -
136A MET* 2.9 39.7 + - + +
137A LYS* 3.9 6.3 - - - +
139A ALA* 1.3 74.6 - - + +
141A GLN* 1.3 65.1 + - - +
143A GLY 3.5 0.4 + - - -
144A HIS 3.4 16.1 + - - -
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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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124A LEU* 3.3 29.0 - - + +
128A CYS* 4.4 4.5 - - - -
137A LYS* 2.9 24.7 + - + +
138A ALA* 2.8 11.3 + - - +
140A LEU* 1.3 76.6 - - - +
142A GLU* 1.3 65.7 + - + +
144A HIS* 3.5 1.0 + - - -
145A GLN* 3.1 24.9 + - - +
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Residues in contact with GLU 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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81A PHE* 3.3 25.3 - - + -
83A ARG* 3.2 38.9 + - - +
85A LEU* 5.8 0.5 - - - +
138A ALA* 2.6 43.4 + - + +
139A ALA* 3.4 6.3 + - - -
141A GLN* 1.3 73.4 - - + +
143A GLY* 1.3 56.8 + - - +
145A GLN* 3.3 8.5 - - - +
146A PHE* 2.7 32.2 + - - +
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Residues in contact with GLY 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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14A ILE* 5.4 1.3 - - - -
31A PHE* 4.7 6.3 - - - -
81A PHE* 3.5 3.3 - - - -
100A LEU* 3.5 24.4 - - - +
139A ALA 3.1 18.3 + - - -
140A LEU* 3.8 3.6 - - - -
141A GLN 3.2 0.8 - - - -
142A GLU* 1.3 76.8 - - - +
144A HIS* 1.3 56.4 + - - +
147A LEU* 3.0 38.2 + - - +
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Residues in contact with HIS 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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26A ASN 5.2 8.1 + - - -
27A ASN* 5.9 1.4 - - - -
28A ALA* 5.8 2.6 + - - +
29A ILE* 4.0 39.7 + - + +
31A PHE* 4.1 16.3 - + + -
124A LEU* 4.2 21.5 - - + +
140A LEU 3.4 14.5 + - - +
141A GLN 4.2 2.9 - - - +
142A GLU 3.4 0.2 - - - -
143A GLY* 1.3 74.3 - - - +
145A GLN* 1.3 63.2 + - - +
147A LEU* 4.3 6.4 - - - +
148A CYS* 3.2 38.6 + - - +
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Residues in contact with GLN 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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141A GLN* 3.1 24.2 + - - +
142A GLU* 3.1 11.4 + - - +
144A HIS* 1.3 81.7 + - - +
146A PHE* 1.3 62.6 + - - +
148A CYS* 3.7 11.1 + - - +
149A SER* 3.7 9.4 + - - -
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Residues in contact with PHE 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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78A ILE* 3.5 15.9 - - + -
79A GLU 3.5 17.3 - - - -
80A GLY* 3.7 23.3 - - - -
81A PHE* 3.4 28.7 - + + -
100A LEU* 3.9 6.5 - - + -
142A GLU 2.7 19.5 + - - +
143A GLY 3.9 0.9 - - - +
145A GLN* 1.3 70.7 - - - +
147A LEU* 1.3 59.1 + - - +
148A CYS 3.0 2.0 - - - -
149A SER* 2.6 38.5 + - - -
150A ILE* 3.2 37.2 - - + +
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Residues in contact with LEU 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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16A PHE* 3.1 48.5 - - + -
29A ILE* 5.0 15.5 - - + -
31A PHE* 5.4 2.0 - - + -
78A ILE* 3.5 19.5 - - + -
100A LEU* 3.3 22.4 - - + -
143A GLY 3.0 24.4 + - - +
144A HIS* 4.3 5.4 - - - +
146A PHE* 1.3 76.6 - - - +
148A CYS* 1.3 61.6 + - - +
150A ILE* 3.1 43.1 + - + +
151A GLU* 4.4 1.9 + - - +
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Residues in contact with CYS 148 (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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144A HIS* 3.2 37.9 + - + +
145A GLN* 3.8 12.8 - - - +
146A PHE 3.0 0.8 - - - -
147A LEU* 1.3 76.6 - - - +
149A SER* 1.3 57.6 + - - +
150A ILE 3.7 5.0 + - - +
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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