Contacts of the strand formed by residues 142 - 152 (chain A) in PDB entry 4JZJ
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 THR 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLY* 1.3 84.2 + - - +
143A ALA* 1.3 61.0 + - - +
190A THR* 4.0 26.2 - - + +
191A VAL 3.7 13.2 - - - +
192A PRO* 4.8 0.9 - - + -
193A SER* 3.8 1.6 - - - -
122B PHE* 3.4 22.8 - - + -
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Residues in contact with ALA 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 PRO* 4.7 8.3 - - + -
142A THR* 1.3 75.5 - - - +
144A ALA* 1.3 59.0 + - - +
190A THR* 3.2 5.2 - - - -
191A VAL* 2.8 41.7 + - + +
193A SER* 3.6 16.0 + - - +
196A LEU* 4.2 33.9 - - + -
122B PHE* 4.4 1.3 - - - -
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Residues in contact with ALA 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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133A PRO* 3.2 23.2 - - - +
143A ALA* 1.3 75.8 - - - +
145A LEU* 1.3 60.6 + - - +
189A VAL 3.3 9.2 - - - +
190A THR* 4.0 9.2 - - + -
122B PHE* 3.5 40.2 - - + -
124B PHE* 3.3 18.6 - - + -
141B LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 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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131A LEU 3.3 13.9 - - - +
133A PRO* 4.1 11.4 - - + -
144A ALA* 1.3 73.9 - - - +
146A GLY* 1.3 58.4 + - - +
161A TRP* 3.7 21.3 - - + -
188A VAL* 3.5 3.9 - - - +
189A VAL* 2.9 50.3 + - + +
191A VAL* 4.0 17.9 - - + -
196A LEU* 4.1 13.2 - - + -
201A TYR* 4.0 36.8 - - + -
218A VAL* 3.8 19.3 - - + +
220A PRO* 6.0 0.9 - - + -
124B PHE* 3.7 7.0 - - - -
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Residues in contact with GLY 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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131A LEU* 2.8 39.8 + - - +
145A LEU* 1.3 78.5 - - - +
147A CYS* 1.3 59.5 + - - -
161A TRP* 3.4 11.9 - - - -
187A SER 3.2 13.2 - - - -
188A VAL* 4.1 1.8 - - - -
218A VAL* 3.5 15.9 - - - +
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Residues in contact with CYS 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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128A VAL* 4.5 4.9 - - + -
129A PHE 3.5 5.6 - - - +
131A LEU* 4.1 3.7 - - - +
146A GLY* 1.3 76.2 - - - -
148A LEU* 1.3 60.1 + - - +
149A VAL* 3.6 11.8 + - + +
159A VAL* 5.2 0.7 - - + -
161A TRP* 3.8 6.9 - - + -
186A SER* 3.2 5.4 - - - -
187A SER* 2.9 34.7 + - - +
203A CYS* 2.0 55.0 - - + -
205A VAL* 5.1 0.2 - - + -
216A LYS* 4.4 7.9 - - - -
218A VAL* 4.1 11.9 - - - -
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Residues in contact with LEU 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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127A SER 3.5 0.5 - - - +
128A VAL* 3.4 4.7 - - - -
129A PHE* 2.6 49.8 + - + +
131A LEU* 4.1 12.2 - - + +
147A CYS* 1.3 71.7 - - - +
149A VAL* 1.3 58.2 + - - +
150A LYS* 3.5 25.5 + - + +
184A SER* 6.3 0.9 - - - -
185A LEU 3.8 7.2 - - - +
186A SER* 3.6 22.2 - - - -
130B GLN* 4.4 6.7 - - - +
137B SER* 3.5 34.5 - - - +
139B VAL* 4.3 19.7 - - + -
184B THR* 5.0 8.3 - - + +
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Residues in contact with VAL 149 (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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126A PRO* 3.5 27.6 - - + -
127A SER 3.8 2.0 - - - -
128A VAL* 4.3 4.9 - - + -
147A CYS* 4.3 11.0 - - + +
148A LEU* 1.3 74.3 - - - +
150A LYS* 1.3 58.3 + - - +
152A TYR* 3.9 13.1 - - + -
157A VAL* 4.2 5.8 - - + -
159A VAL* 4.3 6.7 - - + -
184A SER* 3.4 4.0 - - - -
185A LEU* 2.7 57.7 + - + +
187A SER 5.4 0.4 - - - +
205A VAL* 3.8 38.6 - - + -
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Residues in contact with LYS 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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126A PRO* 3.3 2.5 - - - +
127A SER* 2.7 51.9 + - - +
129A PHE* 4.4 8.3 - - + -
148A LEU* 3.5 15.9 + - + +
149A VAL* 1.3 73.7 - - - +
151A ASP* 1.3 80.7 + - + +
152A TYR* 3.8 1.8 - - - -
178A GLN* 3.7 16.0 - - - +
184A SER* 3.2 17.8 - - - +
130B GLN* 3.4 24.9 - - - +
135B THR* 4.7 9.4 - - - -
137B SER* 3.1 21.6 + - - +
184B THR* 5.1 2.6 - - - +
186B THR* 3.3 19.4 - - - +
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Residues in contact with ASP 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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124A LYS* 3.3 30.8 + - - +
125A GLY 3.4 7.1 - - - +
127A SER* 5.4 3.1 - - - +
150A LYS* 1.3 101.7 - - + +
152A TYR* 1.3 57.3 + - - +
178A GLN* 3.5 18.1 - - - +
180A SER* 5.0 3.1 + - - -
182A LEU* 3.9 26.9 - - + +
183A TYR 3.0 17.3 + - - -
184A SER* 3.3 0.6 + - - -
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Residues in contact with TYR 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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124A LYS 3.5 6.5 - - - +
126A PRO* 3.4 42.8 - - + -
149A VAL* 3.9 26.2 - - + -
151A ASP* 1.3 75.4 - - - +
153A PHE* 1.3 63.4 + - - +
154A PRO 3.4 27.4 - - - -
155A GLU* 3.5 10.4 + - - -
157A VAL* 3.9 17.9 - - + +
175A ALA* 3.3 26.2 - - - +
182A LEU* 3.7 3.7 - - - -
183A TYR* 2.8 56.6 + - + +
184A SER* 4.3 2.5 - - - -
185A LEU* 3.4 13.9 - - + +
207A HIS* 3.9 6.3 - + + -
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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