Contacts of the helix formed by residues 130 - 147 (chain B) in PDB entry 1XUD
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 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B TYR* 5.2 0.2 - - - -
129B MET* 1.3 76.7 - - - +
131B HIS* 1.3 66.0 + - - +
132B SER* 3.5 9.4 + - - -
133B GLU* 2.9 43.1 + - - +
134B VAL* 3.0 21.8 + - - +
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 3.6 53.1 - + + +
129B MET 5.7 0.7 - - - -
130B THR* 1.3 73.6 - - - +
132B SER* 1.3 57.1 + - - +
134B VAL 3.3 0.5 + - - -
135B GLU* 2.9 44.8 + - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.1 9.1 + - - -
131B HIS* 1.3 80.0 - - - +
133B GLU* 1.3 57.5 + - - +
135B GLU* 3.4 11.2 + - - +
136B LYS* 2.9 60.4 + - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP 4.9 0.3 - - - +
129B MET* 3.5 26.3 - - + +
130B THR* 2.9 48.8 + - + +
132B SER* 1.3 76.4 - - - +
134B VAL* 1.3 57.8 + - - +
136B LYS* 3.4 8.0 + - + +
137B ALA* 2.9 30.1 + - - +
209B SER* 4.1 16.3 + - - +
210B SER* 3.9 18.7 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.4 2.2 - - + -
125B TYR* 3.6 34.1 - - + -
126B THR* 3.9 19.5 - - + +
129B MET* 3.8 26.9 - - + +
130B THR 3.0 13.7 + - - +
131B HIS 3.7 0.9 - - - +
133B GLU* 1.3 76.8 - - - +
135B GLU* 1.3 63.0 + - - +
137B ALA* 3.2 2.4 + - - +
138B PHE* 3.1 51.3 + - + -
167B PHE* 4.4 6.3 - - + -
216B LEU* 4.2 6.7 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR* 5.1 1.6 + - - -
122B ILE* 3.9 13.2 - - + +
125B TYR* 2.8 31.0 + - + +
131B HIS* 2.9 29.6 + - - +
132B SER* 3.7 11.2 - - - +
134B VAL* 1.3 76.9 - - - +
136B LYS* 1.3 62.3 + - + +
138B PHE* 3.5 1.7 + - - +
139B LYS* 3.0 25.2 + - - +
155B ARG* 3.1 33.0 + - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 2.9 39.1 + - - +
133B GLU* 3.8 6.5 - - + +
135B GLU* 1.3 77.2 - - + +
137B ALA* 1.3 57.7 + - - +
139B LYS* 3.3 8.1 + - + +
140B LYS* 2.9 32.3 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLU 2.9 18.8 + - - +
134B VAL 3.5 4.5 - - - +
136B LYS* 1.3 77.0 - - - +
138B PHE* 1.3 59.1 + - - +
140B LYS* 3.6 4.9 - - - +
141B ALA* 2.9 27.5 + - - +
209B SER* 4.4 8.5 - - - +
216B LEU* 4.1 16.6 - - + -
217B PHE* 3.7 35.8 - - + +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR* 4.9 3.1 - - + -
122B ILE* 3.7 26.7 - - + -
134B VAL* 3.1 43.0 + - + +
135B GLU 4.1 2.2 - - - +
137B ALA* 1.3 73.0 - - - +
139B LYS* 1.3 65.0 + - - +
141B ALA* 3.2 3.8 + - - +
142B PHE* 3.0 34.2 + - + -
165B ILE* 3.5 33.4 - - + -
167B PHE* 3.8 22.2 - + - -
201B PHE* 3.8 18.4 - + - -
216B LEU* 4.0 13.5 - - + -
220B ALA* 3.7 28.5 - - + -
224B PHE* 3.8 8.7 - + - -
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR* 4.1 18.1 + - - +
135B GLU 3.0 17.7 + - - +
136B LYS* 3.7 8.5 - - + +
137B ALA 3.3 0.2 - - - -
138B PHE* 1.3 76.3 - - - +
140B LYS* 1.3 62.4 + - - +
142B PHE* 3.4 5.3 + - - +
143B LYS* 3.1 23.2 + - + +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LYS 2.9 18.0 + - - +
137B ALA* 3.6 5.2 - - - +
139B LYS* 1.3 77.8 - - - +
141B ALA* 1.3 61.5 + - - +
143B LYS* 3.2 14.5 + - + +
144B VAL* 3.2 22.1 + - + +
217B PHE* 3.3 44.6 - - + -
252B PHE* 4.5 9.6 + - - +
3001B PB4 4.3 21.9 - - - +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA 2.9 17.3 + - - +
138B PHE 3.2 6.7 + - - +
140B LYS* 1.3 78.4 - - - +
142B PHE* 1.3 60.9 + - - +
144B VAL* 3.2 18.9 - - - +
145B TRP* 3.6 12.0 + - - -
217B PHE* 3.6 13.9 - - - +
220B ALA* 3.7 6.3 - - + -
221B ALA* 3.6 21.0 - - - +
224B PHE* 3.6 23.5 - - + -
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Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TYR* 3.3 56.8 - + + -
138B PHE 3.0 24.6 + - - +
139B LYS* 3.8 5.2 - - - +
140B LYS 3.3 0.2 - - - -
141B ALA* 1.3 74.5 - - - +
143B LYS* 1.3 66.0 + - - +
145B TRP* 3.1 6.2 + + - +
146B SER* 3.1 21.3 + - - -
153B PHE* 3.5 47.4 - + + -
163B ILE* 3.8 26.5 - - + -
165B ILE* 3.9 4.9 - - + -
224B PHE* 3.5 46.7 - + + -
228B LEU* 6.5 0.2 - - + -
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LYS* 3.1 15.5 + - + +
140B LYS* 3.2 16.6 + - + +
142B PHE* 1.3 73.5 - - - +
144B VAL* 1.3 66.8 + - - +
146B SER* 3.2 11.0 - - - +
147B ASP* 2.9 56.6 + - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS* 3.2 16.0 + - + +
141B ALA* 3.2 11.9 - - - +
142B PHE 3.1 0.4 - - - -
143B LYS* 1.3 78.6 - - - +
145B TRP* 1.3 71.2 + - + +
147B ASP* 4.0 7.6 + - - +
148B VAL* 3.8 6.8 - - - +
217B PHE* 3.7 26.5 - - + -
221B ALA* 4.4 3.4 - - + -
239B LEU* 4.4 4.3 - - + -
252B PHE* 3.8 19.1 - - + -
254B LEU* 3.7 46.1 - - + +
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Residues in contact with TRP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA 3.6 15.5 + - - -
142B PHE* 3.1 8.9 + + - +
144B VAL* 1.3 80.5 - - + +
146B SER* 1.3 61.6 + - - +
147B ASP 3.1 2.2 - - - -
148B VAL* 3.3 9.9 + - - +
149B THR* 2.8 25.2 + - - +
151B LEU* 4.9 2.7 - - + -
153B PHE* 4.5 4.9 - + + -
221B ALA* 3.0 30.1 + - - +
224B PHE* 3.8 9.5 - - + +
225B GLY* 3.6 19.3 - - - +
228B LEU* 3.6 29.8 - - + -
230B LEU* 3.7 19.3 - - + -
239B LEU* 3.5 22.4 - - + -
240B MET* 4.3 6.1 - - - -
254B LEU* 4.1 15.3 - - + -
258B ASP* 4.0 19.1 - - + -
262B ILE* 3.7 37.9 - - + -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B PHE 3.1 9.1 + - - -
143B LYS* 3.2 23.7 + - - +
145B TRP* 1.3 78.5 - - - +
147B ASP* 1.3 61.6 + - - +
149B THR* 3.1 21.9 - - - +
151B LEU 3.2 27.1 - - - +
152B ASN* 4.8 3.1 + - - -
153B PHE* 4.0 14.6 - - - -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LYS* 2.9 63.8 + - - +
144B VAL* 4.1 6.9 - - - +
145B TRP 3.1 0.4 - - - -
146B SER* 1.3 81.4 + - - +
148B VAL* 1.3 65.4 + - + +
149B THR 3.7 0.4 - - - -
269B GLY* 5.4 3.4 - - - -
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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
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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