Contacts of the helix formed by residues 134 - 148 (chain A) in PDB entry 4JU8
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 GLU 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TYR* 2.5 33.9 + - - -
129A PRO* 3.9 9.9 - - + -
130A ALA* 2.8 31.0 + - - +
131A SER* 3.2 19.9 + - - +
132A ALA 3.0 0.8 - - - -
133A ALA* 1.3 78.2 - - - +
135A VAL* 1.3 64.2 + - - +
136A PRO 3.4 0.4 - - - -
137A HIS* 3.1 23.2 + - + +
138A ALA* 2.9 22.1 + - - +
141A ARG* 4.3 6.9 + - - -
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Residues in contact with VAL 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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4A VAL* 3.7 16.8 - - + -
8A THR* 4.0 5.2 - - + +
129A PRO* 4.0 17.3 - - + -
131A SER 3.9 5.2 - - - +
132A ALA 3.0 18.8 + - - +
134A GLU* 1.3 76.8 - - - +
136A PRO* 1.3 61.6 - - + +
138A ALA* 3.1 2.6 + - - +
139A MET* 2.8 28.0 + - + +
156A LEU* 4.7 3.3 - - + +
158A VAL* 3.9 20.0 - - + -
162A ASP* 3.5 27.1 - - + +
163A TRP* 3.9 25.4 - - + -
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Residues in contact with PRO 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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4A VAL* 4.1 12.3 - - + -
7A THR* 3.8 32.5 - - + -
8A THR* 3.8 20.2 - - - +
11A LEU* 3.3 15.5 - - + +
132A ALA 4.0 3.8 - - - +
133A ALA 3.5 14.1 - - - +
135A VAL* 1.3 93.7 - - + +
137A HIS* 1.3 56.8 + - - +
139A MET* 3.2 4.3 + - + -
140A SER* 2.9 24.9 + - - -
167A ALA* 4.9 2.9 - - + -
171A SER* 4.1 8.3 - - - +
174A LEU* 3.6 13.4 - - + +
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Residues in contact with HIS 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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133A ALA 5.0 1.3 + - - +
134A GLU* 3.1 25.0 + - + +
136A PRO* 1.3 78.8 - - - +
138A ALA* 1.3 58.5 + - - +
140A SER* 3.2 5.2 + - - -
141A ARG* 2.9 58.7 + - + +
171A SER* 5.1 1.7 + - - +
174A LEU* 3.6 30.8 - - + +
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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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125A TRP* 3.6 7.6 - - - -
127A TYR* 4.0 15.0 - - + -
129A PRO* 3.7 25.1 - - + -
134A GLU* 2.9 14.2 + - - +
135A VAL 3.5 7.4 - - - +
137A HIS* 1.3 76.2 + - - +
139A MET* 1.3 57.5 + - - +
141A ARG* 3.3 14.5 + - - +
142A ALA* 2.9 24.3 + - - +
156A LEU* 3.7 15.2 - - + +
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Residues in contact with MET 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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8A THR* 3.8 27.6 - - + -
11A LEU* 3.9 13.9 - - + -
12A LEU* 4.2 12.8 - - + -
31A PHE* 5.3 0.4 - - + -
66A PHE* 3.8 35.0 - - + -
93A ILE* 4.3 10.8 - - - -
95A THR* 3.9 16.2 - - + -
135A VAL* 2.8 14.0 + - + +
136A PRO* 3.2 10.5 + - + +
138A ALA* 1.3 74.1 - - - +
140A SER* 1.3 58.7 + - - +
142A ALA* 3.1 3.4 + - - +
143A ILE* 2.9 30.3 + - + +
156A LEU* 3.9 19.9 - - + +
158A VAL* 5.6 0.2 - - + -
163A TRP* 4.6 13.0 - - + -
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Residues in contact with SER 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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11A LEU* 3.6 15.5 - - - +
136A PRO 2.9 13.4 + - - -
137A HIS* 3.2 11.5 + - - -
139A MET* 1.3 75.2 - - - +
141A ARG* 1.3 63.2 + - - +
143A ILE* 3.2 6.3 + - - +
144A HIS* 3.0 46.0 + - - -
174A LEU* 3.8 30.9 + - - +
177A ARG* 4.4 7.8 + - - -
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Residues in contact with ARG 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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125A TRP* 3.5 45.1 - - + +
127A TYR* 4.0 25.3 + - - -
134A GLU* 4.3 4.6 + - - -
137A HIS* 2.9 46.6 + - + +
138A ALA* 3.5 10.5 - - - +
140A SER* 1.3 77.7 + - - +
142A ALA* 1.3 55.9 + - - +
144A HIS* 3.4 3.8 + - - +
145A MET* 2.8 38.5 + - + +
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Residues in contact with ALA 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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93A ILE* 4.1 15.0 - - + -
125A TRP* 3.7 17.8 - - + -
138A ALA 2.9 14.0 + - - +
139A MET* 3.1 13.4 + - - +
141A ARG* 1.3 72.7 - - - +
143A ILE* 1.3 67.2 + - - +
145A MET* 3.9 0.6 - - - -
146A ALA* 3.0 20.8 + - - +
154A VAL* 3.4 25.3 - - + +
155A TYR 5.8 0.2 - - - +
156A LEU* 4.8 11.2 - - + -
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Residues in contact with ILE 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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11A LEU* 4.1 23.8 - - + -
12A LEU* 4.0 24.0 - - + -
15A GLN* 4.1 38.8 - - + +
17A ILE* 4.1 5.8 - - + -
64A PRO* 5.3 3.6 - - + -
93A ILE* 3.9 26.4 - - + +
139A MET* 2.9 23.5 + - + +
140A SER* 3.6 7.0 - - - +
142A ALA* 1.3 77.5 - - - +
144A HIS* 1.3 68.5 + - + +
146A ALA* 3.5 2.4 + - - +
147A SER* 2.8 35.8 + - - +
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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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11A LEU* 6.1 0.4 - - - +
15A GLN* 3.5 29.3 + - - +
140A SER* 3.0 39.6 + - - +
141A ARG* 4.2 4.0 - - - +
143A ILE* 1.3 77.4 - - + +
145A MET* 1.3 61.8 + - - +
147A SER* 3.1 6.2 + - - -
148A MET* 2.9 45.5 + - + +
174A LEU 5.2 0.2 + - - -
177A ARG* 3.7 40.8 - - - +
179A VAL* 3.5 33.8 - - + +
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Residues in contact with MET 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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124A LYS* 2.7 67.2 + - + +
125A TRP* 4.1 26.5 - - + -
141A ARG* 2.8 24.7 + - + +
142A ALA* 4.0 0.9 - - - +
144A HIS* 1.3 77.5 - - - +
146A ALA* 1.3 57.9 + - - +
147A SER 3.4 0.2 + - - -
148A MET* 3.6 21.0 + - + -
154A VAL* 3.8 17.7 - - + -
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Residues in contact with ALA 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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64A PRO* 5.1 0.4 - - + -
91A PRO* 3.4 8.5 - - + +
92A LEU 4.0 12.8 - - - +
93A ILE* 4.0 11.2 - - + -
142A ALA 3.0 17.4 + - - +
143A ILE 3.8 4.5 - - - +
145A MET* 1.3 77.1 - - - +
147A SER* 1.3 59.6 + - - +
151A GLN* 3.4 11.4 - - - +
152A GLY 3.2 40.6 + - - +
154A VAL* 3.6 14.5 - - + +
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Residues in contact with SER 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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64A PRO* 3.5 27.2 - - - +
91A PRO* 4.6 1.1 - - - -
143A ILE* 2.8 24.7 + - - +
144A HIS* 3.1 9.0 + - - -
146A ALA* 1.3 78.2 - - - +
148A MET* 1.3 64.2 + - - +
149A ALA 3.7 0.7 + - - -
151A GLN* 2.9 28.6 + - - +
181A SER* 4.8 1.0 + - - -
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Residues in contact with MET 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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124A LYS* 2.9 26.9 + - - +
144A HIS* 2.9 30.7 + - + +
145A MET* 3.6 30.3 - - - -
146A ALA 3.6 0.4 - - - -
147A SER* 1.3 78.4 - - - +
149A ALA* 1.3 65.3 + - - +
150A PRO 3.1 7.0 - - - -
151A GLN* 3.2 2.6 + - - -
179A VAL* 3.7 34.3 - - + +
180A SER 6.0 0.2 - - - +
181A SER* 3.8 15.9 - - - +
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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