Contacts of the helix formed by residues 132 - 142 (chain Z) 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 SER 132 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24Y ASN* 5.0 5.4 + - - -
2Z THR* 4.6 2.6 - - - +
127Z SER* 3.4 32.8 - - - -
128Z VAL* 3.8 4.7 - - - +
129Z GLY 2.9 21.0 + - - -
130Z SER 3.2 1.2 + - - -
131Z GLY* 1.4 77.4 - - - +
133Z VAL* 1.3 66.9 + - - +
135Z ALA* 3.5 8.1 - - - +
136Z TYR* 2.9 43.5 + - - -
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Residues in contact with VAL 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K PHE* 3.4 41.2 - - + +
138K LEU* 3.4 42.1 - - + +
24Y ASN* 5.0 4.7 - - + +
25Y ILE* 3.9 20.9 - - + -
26Y VAL* 4.9 8.1 - - + -
130Z SER 3.8 17.0 - - - +
132Z SER* 1.3 84.9 + - - +
134Z TYR* 1.3 70.9 + - + +
136Z TYR* 4.1 3.3 - - - +
137Z GLY 4.0 6.9 + - - -
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Residues in contact with TYR 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ALA 4.9 0.3 - - - -
32J GLN* 3.1 57.6 + - + +
137K PHE* 3.2 32.1 - - - -
140K LEU* 5.7 0.2 - - + -
141K SER* 2.8 40.4 + - - -
130Z SER 4.2 2.0 - - - -
131Z GLY* 3.1 32.3 + - - +
133Z VAL* 1.3 86.5 - - + +
135Z ALA* 1.3 62.4 + - - +
136Z TYR 3.3 0.4 - - - -
137Z GLY 3.5 4.0 + - - -
138Z VAL* 3.5 7.3 - - - +
159Z ALA 5.2 0.2 - - - -
162Z GLN 4.1 3.1 - - - +
163Z ALA* 3.9 25.8 - - - -
166Z ARG* 4.0 12.6 - - + -
167Z ASP* 3.9 24.3 + - + -
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Residues in contact with ALA 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z THR* 4.1 13.5 - - + -
4Z LEU* 4.8 6.3 - - + -
127Z SER* 3.5 25.2 + - - +
131Z GLY 3.1 12.6 + - - +
132Z SER* 3.1 8.0 + - - +
134Z TYR* 1.3 75.4 - - - +
136Z TYR* 1.3 57.9 + - - +
138Z VAL* 3.7 1.1 + - - +
139Z MET* 3.2 26.9 + - - +
159Z ALA* 3.9 28.1 - - - +
163Z ALA* 4.2 1.1 - - + -
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Residues in contact with TYR 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K LEU* 5.1 1.3 - - + -
166K GLU* 4.2 6.5 - - - +
170K ARG* 2.1 46.2 - - - +
24Y ASN* 5.3 1.1 - - - -
26Y VAL* 4.2 21.3 - - + -
28Y MET* 4.5 14.9 + - + +
113Z TYR* 5.7 0.7 - - - -
125Z THR* 4.1 3.6 - - + -
126Z PHE* 3.6 26.2 - - - -
127Z SER* 3.1 46.0 + - - -
132Z SER* 2.9 33.1 + - - +
133Z VAL* 4.1 9.0 - - - +
135Z ALA* 1.3 74.8 - - - +
137Z GLY* 1.3 62.9 + - - +
139Z MET* 3.2 17.7 + - + +
140Z ASP* 3.2 21.3 + - - -
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Residues in contact with GLY 137 (chain Z).
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 4.2 1.1 - - - -
141K SER* 4.0 6.1 - - - -
142K ILE* 3.4 26.0 - - - +
166K GLU* 3.7 20.1 + - - -
133Z VAL 4.0 3.0 + - - -
134Z TYR 3.5 4.2 + - - -
135Z ALA 3.4 0.8 - - - -
136Z TYR* 1.3 80.3 - - - +
138Z VAL* 1.3 57.1 + - - +
140Z ASP 4.0 1.7 + - - -
141Z ARG* 3.1 27.5 + - - +
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Residues in contact with VAL 138 (chain Z).
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* 3.8 17.5 - - - +
142K ILE* 5.1 2.2 - - - +
145K ARG* 4.3 21.3 - - + -
146K TYR* 5.6 3.1 - - + -
134Z TYR 3.5 16.6 + - - +
135Z ALA 4.0 5.4 - - - +
136Z TYR 3.4 0.2 - - - -
137Z GLY* 1.3 73.4 - - - +
139Z MET* 1.3 64.0 - - - +
140Z ASP 3.4 0.2 - - - -
141Z ARG* 3.5 16.4 + - + +
142Z GLY 3.8 4.0 + - - -
155Z LEU* 3.8 9.6 - - + +
158Z ARG* 4.4 10.5 - - + -
159Z ALA* 4.0 24.9 - - + +
162Z GLN* 3.8 24.7 - - + -
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Residues in contact with MET 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z LEU* 3.9 15.7 - - + -
5Z ALA 4.1 3.1 - - - +
6Z PHE* 3.5 49.4 - - + -
125Z THR* 3.3 25.1 - - + -
126Z PHE 3.5 24.7 - - - +
127Z SER* 3.7 9.6 - - - +
135Z ALA 3.2 18.6 + - - +
136Z TYR* 3.2 12.3 + - + +
138Z VAL* 1.3 77.9 - - - +
140Z ASP* 1.4 62.0 + - - +
141Z ARG 3.3 0.3 + - - -
142Z GLY 3.5 0.2 + - - -
143Z TYR* 3.1 31.0 + - + +
155Z LEU* 4.0 10.1 - - - +
159Z ALA* 4.6 4.3 - - + -
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Residues in contact with ASP 140 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K GLU* 3.8 1.8 - - - +
169K LYS* 5.1 15.8 - - + +
170K ARG* 2.1 55.4 + - - +
125Z THR* 4.2 12.3 - - - +
136Z TYR 3.2 10.4 + - - +
137Z GLY 4.0 1.1 + - - +
139Z MET* 1.4 79.6 - - - +
141Z ARG* 1.3 80.3 + - - +
142Z GLY 3.3 0.9 + - - -
143Z TYR* 3.7 21.0 + - - +
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Residues in contact with ARG 141 (chain Z).
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* 3.4 27.3 - - + +
146K TYR* 2.7 37.8 + - + +
162K LYS* 3.0 55.1 + - - +
165K GLU* 3.3 23.1 + - - +
166K GLU* 3.2 29.9 + - - +
169K LYS* 5.4 4.9 - - - +
170K ARG* 5.9 0.2 - - - +
137Z GLY 3.1 19.1 - - - +
138Z VAL 3.6 8.5 - - - +
139Z MET 3.2 0.8 - - - -
140Z ASP* 1.3 102.5 + - - +
142Z GLY* 1.3 56.7 + - - +
143Z TYR 5.0 0.2 - - - -
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Residues in contact with GLY 142 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Z VAL 3.8 3.6 + - - -
139Z MET 3.5 3.2 + - - -
141Z ARG* 1.3 76.9 - - - +
143Z TYR* 1.3 70.1 + - - +
144Z SER* 3.3 5.0 + - - -
147Z LEU* 3.8 15.4 - - - +
155Z LEU* 3.5 20.0 - - - -
158Z ARG* 5.1 7.0 - - - -
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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