Contacts of the helix formed by residues 135 - 146 (chain K) in PDB entry 5A0Q
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 135 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3K TYR* 3.5 18.7 - - - +
133K GLY 3.5 0.4 - - - -
134K TYR* 1.3 78.3 - - - +
136K ALA* 1.4 53.9 + - - +
137K PHE 3.3 1.1 - - - -
138K LEU* 3.3 9.9 + - - +
139K THR* 2.8 35.5 + - - +
167K LEU* 4.1 14.1 - - - -
171K PHE* 4.2 17.2 - - - -
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Residues in contact with ALA 136 (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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32J GLN* 4.3 1.5 + - - +
3K TYR* 3.6 7.2 - - - -
131K ALA* 4.1 9.0 - - + +
132K HIS* 3.8 23.3 - - - +
133K GLY 3.7 18.2 - - - +
134K TYR 3.0 0.6 - - - +
135K GLY* 1.4 72.7 - - - +
137K PHE* 1.4 68.9 + - + +
138K LEU 3.2 1.2 + - - -
139K THR* 3.5 7.4 - - - -
140K LEU* 3.3 34.8 + - + +
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Residues in contact with PHE 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ILE* 5.3 7.9 - - + -
30J GLN* 4.0 28.7 - - + -
32J GLN* 3.1 34.1 - - + -
133K GLY 5.6 1.8 - - - -
134K TYR* 3.6 8.2 + + - +
135K GLY 3.3 0.6 - - - -
136K ALA* 1.4 82.5 - - + +
138K LEU* 1.3 58.4 + - - +
140K LEU 4.8 0.4 + - - -
25Y ILE* 3.8 24.5 - - + -
130Z SER 6.1 0.4 - - - -
133Z VAL* 3.4 28.6 - - + +
134Z TYR* 3.2 36.4 - - - -
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Residues in contact with LEU 138 (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 GLY* 3.3 11.0 + - - +
136K ALA 3.2 0.6 - - - -
137K PHE* 1.3 78.8 - - - +
139K THR* 1.3 60.1 + - + +
140K LEU 3.5 0.4 - - - -
141K SER* 2.9 23.4 + - - -
142K ILE* 4.1 5.7 - - - +
166K GLU* 3.5 26.6 - - + +
167K LEU* 5.4 0.9 - - + -
171K PHE* 3.6 38.4 - - + +
25Y ILE* 3.9 10.1 - - + -
26Y VAL* 3.3 37.9 - - + -
133Z VAL* 3.4 40.1 - - + +
136Z TYR* 5.1 1.8 - - + -
137Z GLY* 4.2 4.2 - - - -
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Residues in contact with THR 139 (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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3K TYR* 2.7 39.3 + - + +
5K ILE* 5.3 0.9 - - - -
131K ALA* 4.2 2.6 - - - +
135K GLY 2.8 19.4 + - - +
136K ALA* 3.5 4.2 - - - -
138K LEU* 1.3 72.9 - - - +
140K LEU* 1.3 64.8 + - - +
141K SER 3.2 2.7 - - - -
142K ILE* 3.1 21.3 + - - +
143K LEU* 3.3 12.9 + - - +
163K CYS* 3.9 28.8 - - + +
166K GLU* 3.9 14.8 - - + -
167K LEU* 4.1 7.9 - - + -
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Residues in contact with LEU 140 (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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32J GLN* 3.3 31.0 - - - +
34J VAL* 6.4 0.9 - - - -
5K ILE* 6.2 0.4 - - - -
117K TYR* 6.3 1.3 - - + -
129K PHE* 4.2 12.8 - - + +
130K ALA* 4.1 11.9 - - - -
131K ALA* 3.9 37.9 - - + +
136K ALA* 3.3 23.3 + - + +
137K PHE 5.5 0.9 - - - +
138K LEU 3.5 0.6 - - - -
139K THR* 1.3 79.2 + - - +
141K SER* 1.3 56.7 + - - +
143K LEU* 3.7 6.5 + - + -
144K ASP* 2.9 30.3 + - - +
134Z TYR* 5.7 0.7 - - + -
166Z ARG* 3.8 23.8 - - + +
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Residues in contact with SER 141 (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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138K LEU 2.9 19.9 + - - -
140K LEU* 1.3 76.6 - - - +
142K ILE* 1.3 62.5 + - - -
144K ASP* 4.2 4.9 - - - -
145K ARG* 3.1 24.6 + - - +
134Z TYR* 2.8 48.7 + - - -
137Z GLY* 4.0 6.2 - - - -
138Z VAL* 3.8 9.9 - - - +
162Z GLN* 3.5 12.6 + - - +
166Z ARG* 6.0 3.6 - - - +
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Residues in contact with ILE 142 (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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138K LEU 4.1 0.4 - - - +
139K THR* 3.1 13.6 + - - +
141K SER* 1.3 75.3 - - - +
143K LEU* 1.3 58.5 + - - +
145K ARG* 3.3 1.6 + - - -
146K TYR* 2.9 61.4 + - + +
159K LEU* 5.6 2.0 - - + +
162K LYS* 5.0 5.4 - - + -
163K CYS* 4.1 21.3 - - - -
166K GLU* 3.7 24.9 - - + -
137Z GLY* 3.4 28.9 - - - +
138Z VAL* 5.0 0.9 - - - -
141Z ARG* 3.4 38.8 - - - +
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Residues in contact with LEU 143 (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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5K ILE* 3.3 32.1 - - + -
6K GLY 3.7 5.8 - - - +
7K ILE* 3.8 13.0 - - + -
129K PHE* 3.6 34.9 - - + -
130K ALA 4.5 1.6 - - - +
139K THR 3.3 10.8 + - - +
140K LEU* 4.0 7.0 - - + +
142K ILE* 1.3 80.1 - - - +
144K ASP* 1.3 57.9 + - - +
146K TYR* 4.1 2.2 - - - +
147K TYR* 3.1 39.9 + - + +
159K LEU* 3.8 36.8 - - + -
163K CYS* 4.3 10.5 - - - -
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Residues in contact with ASP 144 (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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129K PHE* 3.4 25.5 - - + -
140K LEU 2.9 20.6 + - - +
141K SER* 3.9 2.7 - - - +
142K ILE 3.3 0.2 - - - -
143K LEU* 1.3 75.7 - - - +
145K ARG* 1.3 63.0 + - - +
147K TYR* 4.2 7.4 - - - +
162Z GLN* 2.8 27.1 + - - +
165Z TYR* 3.0 41.4 + - - -
166Z ARG* 3.9 11.4 + - + +
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Residues in contact with ARG 145 (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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141K SER 3.1 17.5 + - - +
142K ILE 3.7 3.4 - - - +
144K ASP* 1.3 77.3 - - - +
146K TYR* 1.3 77.5 + - + +
147K TYR 4.2 2.9 - - - +
148K THR* 5.8 0.7 - - - +
138Z VAL* 4.3 14.6 - - + -
158Z ARG* 3.7 43.1 - - - +
161Z TYR* 4.0 18.2 - - - -
162Z GLN* 3.4 36.4 + - + +
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Residues in contact with TYR 146 (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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142K ILE* 2.9 46.2 + - + +
145K ARG* 1.3 92.4 - - + +
147K TYR* 1.3 64.5 + - - +
148K THR* 3.6 11.8 + - - +
155K ARG* 5.7 6.7 - - - -
159K LEU* 3.7 22.4 - - + -
162K LYS* 3.6 29.2 + - + -
138Z VAL* 5.6 4.0 - - + -
141Z ARG* 2.7 42.6 + - + +
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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