Contacts of the helix formed by residues 139 - 154 (chain A) in PDB entry 4JYY
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.3 3.6 - - - -
134A ASP* 3.4 13.6 + - - +
137A PHE* 3.2 4.4 + - - +
138A GLY* 1.3 78.8 - - - +
140A PHE* 1.3 66.5 + - - +
141A GLU* 3.5 7.8 + - - +
142A LYS* 3.1 31.2 + - - +
143A PHE* 3.1 21.7 + - - +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A PRO* 3.6 24.5 - - + -
133A ILE* 3.9 17.9 - - + -
134A ASP* 3.4 9.3 + - - +
139A SER* 1.3 74.1 - - - +
141A GLU* 1.3 62.7 + - - +
143A PHE* 3.3 17.6 + + - +
144A LYS* 2.9 46.5 + - + +
215A PHE* 4.9 5.2 - + - -
220A TRP* 3.4 44.2 - + - -
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Residues in contact with GLU 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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139A SER* 3.1 8.4 + - - +
140A PHE* 1.3 85.7 - - - +
142A LYS* 1.3 58.7 + - + +
144A LYS* 3.3 22.0 + - - +
145A GLN* 3.0 58.0 + - - +
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Residues in contact with LYS 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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137A PHE* 3.3 27.4 - - - +
138A GLY* 4.9 7.4 - - - -
139A SER* 3.1 22.7 + - - +
141A GLU* 1.3 74.6 - - + +
143A PHE* 1.3 67.1 + - - +
145A GLN* 3.4 10.6 + - - +
146A GLU* 3.1 23.9 + - - +
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Residues in contact with PHE 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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133A ILE* 3.8 11.2 - - + -
137A PHE* 3.6 41.1 - + + +
139A SER 3.1 10.0 + - - +
140A PHE* 3.5 25.8 - + - +
142A LYS* 1.3 76.6 - - - +
144A LYS* 1.3 72.2 + - - +
146A GLU* 3.2 1.3 + - - -
147A PHE* 2.9 39.8 + + + +
162A LEU* 3.7 29.2 - - + -
172A ILE* 3.7 20.1 - - + +
190A ILE* 3.9 23.6 - - + -
215A PHE* 4.3 7.2 - + - -
220A TRP* 3.7 22.7 - + - -
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Residues in contact with LYS 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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140A PHE* 2.9 36.3 + - + +
141A GLU* 3.7 24.3 + - - +
143A PHE* 1.3 88.8 - - + +
145A GLN* 1.3 57.1 + - + +
147A PHE* 3.4 3.4 + - - +
148A GLN* 3.0 58.6 + - - +
212A ASP* 4.6 11.0 + - - -
215A PHE* 3.9 36.6 - - + +
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Residues in contact with GLN 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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141A GLU* 3.0 49.1 + - - +
142A LYS* 3.8 10.4 - - - +
144A LYS* 1.3 77.4 - - - +
146A GLU* 1.3 60.2 + - - +
148A GLN* 3.5 5.7 + - - +
149A LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 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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137A PHE* 3.6 21.5 - - - -
142A LYS 3.1 17.7 + - - +
143A PHE* 3.7 3.6 - - - +
145A GLN* 1.3 74.0 - - - +
147A PHE* 1.3 66.8 + - - +
149A LYS* 3.3 6.8 + - + +
150A SER* 3.0 33.1 + - - +
172A ILE* 3.8 31.0 + - + +
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Residues in contact with PHE 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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143A PHE* 2.9 37.1 + + + +
144A LYS 3.7 3.8 - - - +
146A GLU* 1.3 77.4 - - - +
148A GLN* 1.3 57.7 + - - +
150A SER* 3.3 2.9 + - - -
151A ALA* 2.8 26.9 + - + +
160A ALA* 3.6 25.5 - - + +
161A TRP* 3.8 30.1 - - - -
162A LEU 3.8 3.4 - - - -
172A ILE* 3.4 18.3 - - + +
190A ILE* 4.1 9.4 - - + -
192A LEU* 3.9 26.0 - - + -
211A ILE* 5.2 0.2 - - + -
214A TRP* 3.7 28.0 - + - -
215A PHE* 3.5 24.7 - + + -
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Residues in contact with GLN 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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144A LYS* 3.0 53.9 + - - +
145A GLN* 3.9 6.7 - - - +
147A PHE* 1.3 72.7 - - - +
149A LYS* 1.3 60.5 + - - +
151A ALA* 3.4 1.6 + - - +
152A LEU* 2.9 31.5 + - - +
208A ASN* 4.6 2.8 + - - +
211A ILE* 3.6 30.3 - - + +
212A ASP* 3.5 26.8 + - - +
215A PHE* 3.5 20.4 - - + -
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A GLN 3.1 19.2 + - - +
146A GLU* 3.6 6.5 - - + +
147A PHE 3.3 0.2 - - - -
148A GLN* 1.3 77.2 - - - +
150A SER* 1.3 62.7 + - - +
152A LEU* 3.2 12.7 + - + +
153A ASP* 2.9 56.8 + - - +
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Residues in contact with SER 150 (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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146A GLU* 3.0 22.8 + - - +
147A PHE 3.6 3.6 - - - -
149A LYS* 1.3 76.2 - - - +
151A ALA* 1.3 63.7 + - - +
153A ASP* 3.2 14.0 + - - +
154A VAL* 3.3 17.3 + - - +
160A ALA* 4.8 1.6 - - - -
172A ILE* 3.5 26.2 + - - +
173A MET 5.6 0.2 - - - -
174A THR* 3.8 17.8 - - - +
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Residues in contact with ALA 151 (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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147A PHE* 2.8 22.3 + - + +
148A GLN 3.7 2.0 - - - +
150A SER* 1.3 74.2 - - - +
152A LEU* 1.3 58.0 + - - +
154A VAL* 3.5 7.7 + - - +
160A ALA* 3.7 22.5 - - + +
192A LEU* 4.1 13.5 - - + -
194A VAL* 4.0 5.9 - - + +
207A ARG* 2.9 25.6 + - - -
211A ILE* 3.6 27.1 - - + -
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Residues in contact with LEU 152 (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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148A GLN 2.9 17.0 + - - +
149A LYS* 3.5 13.7 - - + +
150A SER 3.2 0.4 - - - -
151A ALA* 1.3 77.1 - - - +
153A ASP* 1.3 67.1 + - - +
154A VAL 4.1 1.0 - - - +
207A ARG* 3.2 22.4 + - + +
208A ASN* 3.6 43.1 - - + +
211A ILE* 3.7 8.1 - - + -
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Residues in contact with ASP 153 (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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149A LYS* 2.9 53.0 + - - +
150A SER* 3.2 6.6 + - - +
152A LEU* 1.3 83.8 - - - +
154A VAL* 1.3 67.1 + - - +
155A PHE* 3.1 7.8 + - - +
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Residues in contact with VAL 154 (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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150A SER 3.3 16.5 + - - +
151A ALA* 3.9 6.1 - - - +
152A LEU 3.4 2.6 - - - +
153A ASP* 1.3 76.2 - - - +
155A PHE* 1.3 60.7 + - - +
156A GLY 3.9 12.3 - - - +
157A SER 4.3 3.8 - - - +
158A GLY* 4.0 16.4 - - - +
159A TRP 4.0 8.5 - - - +
174A THR* 3.5 29.6 - - + +
175A THR 4.7 2.9 - - - +
176A PRO* 5.8 0.4 - - + -
194A VAL* 3.8 21.1 - - + -
207A ARG* 2.8 37.2 + - - +
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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