Contacts of the helix formed by residues 146 - 161 (chain K) in PDB entry 5XVO
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 ASN 146 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143K ASP* 3.2 16.8 + - - +
144K PRO 3.2 8.0 - - - +
145K ALA* 1.3 80.4 - - - +
147K ARG* 1.3 64.8 + - - +
148K GLU* 3.2 3.4 - - - +
149K GLY* 3.0 31.7 + - - -
150K HIS* 3.1 16.7 + - - +
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Residues in contact with ARG 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ILE* 4.6 2.0 - - + -
135K MET* 3.3 52.1 - - + +
138K GLU* 2.9 53.4 + - - +
139K LEU* 4.0 9.0 - - + -
143K ASP* 2.8 16.9 + - - +
145K ALA* 3.5 29.5 + - + +
146K ASN* 1.3 76.2 + - - +
148K GLU* 1.3 60.2 - - - +
150K HIS* 3.4 7.3 + - - +
151K ALA* 2.8 33.4 + - - +
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Residues in contact with GLU 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K TRP* 3.9 18.6 - - - -
109K ILE* 4.0 24.1 - - + +
112K LYS* 3.4 29.1 + - - +
113K ILE* 4.1 13.5 - - + +
116K GLN* 4.8 1.6 - - - +
139K LEU* 4.8 0.2 - - - +
143K ASP* 2.8 15.3 + - - +
146K ASN* 4.5 2.4 - - - +
147K ARG* 1.3 78.8 - - - +
149K GLY* 1.3 59.9 + - - +
151K ALA* 3.4 2.8 + - - +
152K ALA* 2.9 28.7 + - + +
203K LYS* 5.3 2.1 + - - -
219K GLU* 3.3 23.4 - - - +
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Residues in contact with GLY 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ASN* 3.0 28.8 + - - -
148K GLU* 1.3 77.4 - - - +
150K HIS* 1.3 60.8 + - - +
152K ALA* 3.8 5.6 - - - +
153K ARG* 3.1 28.1 + - - +
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Residues in contact with HIS 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K MET* 3.2 31.5 - - + +
146K ASN* 3.1 17.1 + - - +
147K ARG* 3.9 7.2 - - - +
149K GLY* 1.3 75.8 - - - +
151K ALA* 1.3 65.5 + - - +
153K ARG* 3.4 12.6 + - + +
154K SER* 3.1 27.7 + - - -
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Residues in contact with ALA 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ILE* 4.3 17.3 - - + -
116K GLN* 4.3 11.4 - - - +
132K LEU* 4.1 17.4 - - + +
135K MET* 3.6 21.4 - - + -
147K ARG 2.8 21.9 + - - +
148K GLU 3.5 5.2 - - - +
150K HIS* 1.3 74.6 - - - +
152K ALA* 1.3 56.9 + - - +
154K SER* 3.5 2.7 + - - -
155K TYR* 2.9 31.0 + - - +
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Residues in contact with ALA 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K LYS* 4.7 9.4 - - - +
116K GLN* 4.2 16.5 + - - +
148K GLU* 2.9 18.1 + - + +
149K GLY* 3.8 7.6 - - - +
150K HIS 3.2 0.2 - - - -
151K ALA* 1.3 74.5 - - - +
153K ARG* 1.3 60.3 + - - +
155K TYR* 3.3 5.9 + - - +
156K PHE* 2.9 47.3 + - + -
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Residues in contact with ARG 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K GLY 3.1 17.6 + - - +
150K HIS* 3.4 14.3 + - + +
152K ALA* 1.3 75.9 - - - +
154K SER* 1.3 56.1 + - - +
156K PHE* 3.9 3.5 - - - +
157K ASN* 2.5 68.5 + - - +
162K ASN* 4.0 8.5 + - - -
164K PHE 4.9 2.1 + - - -
165K THR* 3.9 27.9 - - - +
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Residues in contact with SER 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K LYS* 4.4 12.1 + - - +
131K ALA* 5.6 2.6 - - - +
132K LEU* 4.0 14.8 - - - +
135K MET* 5.2 2.9 - - - -
150K HIS* 3.1 23.0 + - - -
151K ALA* 3.6 5.8 - - - -
153K ARG* 1.3 77.2 - - - +
155K TYR* 1.3 63.2 + - - +
157K ASN* 3.2 8.3 + - - +
158K THR* 2.8 37.7 + - - -
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Residues in contact with TYR 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K GLN* 3.2 61.2 - - + +
119K HIS* 2.8 31.6 + - - +
120K LEU* 3.8 24.6 - - + +
132K LEU* 4.2 6.4 - - + +
151K ALA 2.9 21.2 + - - +
152K ALA* 3.4 5.2 - - - +
154K SER* 1.3 74.1 - - - +
156K PHE* 1.3 89.7 + + - +
158K THR* 3.4 3.2 + - - -
159K LEU* 3.1 37.8 + - + +
223K PRO* 4.3 3.3 - - - +
226K ASP* 2.8 33.1 + - - +
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Residues in contact with PHE 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K GLN* 4.9 3.6 - - - -
152K ALA* 2.9 38.3 + - + +
153K ARG* 4.1 4.3 - - - +
155K TYR* 1.3 100.8 - + - +
157K ASN* 1.3 61.2 + - - +
159K LEU* 4.5 1.8 - - + -
160K PHE* 2.9 54.8 + + - +
164K PHE* 3.9 23.8 - + + +
166K ARG* 3.9 28.0 - - + -
176K LEU* 3.8 19.5 - - + -
180K TYR* 3.7 22.7 - - - -
226K ASP* 4.3 4.7 - - - -
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Residues in contact with ASN 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K LYS* 6.2 1.1 - - - +
153K ARG* 2.5 53.9 + - - +
154K SER* 3.2 7.0 + - - +
156K PHE* 1.3 75.7 - - - +
158K THR* 1.3 58.4 + - - +
161K GLY* 2.6 39.7 + - - +
162K ASN* 3.1 36.0 + - + +
164K PHE 3.3 23.6 + - - -
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Residues in contact with THR 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K LEU* 3.8 14.8 - - + -
125K TYR* 3.5 55.2 + - + -
128K LYS* 3.3 39.4 + - + +
154K SER 2.8 22.2 + - - -
155K TYR* 3.5 6.5 - - - -
157K ASN* 1.3 80.3 - - - +
159K LEU* 1.3 59.9 + - - +
161K GLY 4.4 1.2 + - - -
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Residues in contact with LEU 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K HIS* 3.7 18.6 - - + +
120K LEU* 3.8 19.5 - - + -
123K ARG* 4.2 19.3 - - + -
125K TYR* 4.6 7.3 + - + -
155K TYR* 3.1 49.9 + - + +
157K ASN 3.2 0.2 - - - -
158K THR* 1.3 83.1 - - - +
160K PHE* 1.3 87.1 + - + +
161K GLY 3.6 0.4 - - - -
226K ASP* 5.0 2.9 - - + -
230K TYR* 3.4 38.9 + - + -
233K ARG* 4.8 2.9 + - - -
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Residues in contact with PHE 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K PHE* 2.9 39.2 + + - +
159K LEU* 1.3 90.8 - - + +
161K GLY* 1.3 63.3 + - - +
162K ASN 4.8 0.5 - - - +
164K PHE* 3.5 41.6 + + + +
172K ILE* 3.7 44.2 - - + -
176K LEU* 4.6 5.4 - - + -
226K ASP* 5.1 3.4 - - + -
229K ILE* 4.9 3.6 - - + -
230K TYR* 3.9 36.6 - + + -
233K ARG* 4.1 18.8 - - + +
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Residues in contact with GLY 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K ASN* 2.6 29.4 + - - +
158K THR 4.4 1.9 + - - -
159K LEU 3.6 1.6 - - - -
160K PHE* 1.3 74.7 - - - +
162K ASN* 1.3 70.6 + - - -
164K PHE* 3.3 16.1 + - - +
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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