Contacts of the strand formed by residues 178 - 186 (chain D) 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 SER 178 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL* 4.3 3.3 - - - +
176D SER* 3.6 20.4 + - - -
177D GLN* 1.3 82.4 - - - +
179D SER* 1.3 69.3 + - - +
198D PHE* 3.2 29.2 - - - -
199D VAL 3.2 15.0 - - - -
200D VAL* 4.2 9.0 - - - -
201D PHE* 4.0 4.8 - - - -
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU* 3.8 4.2 - - - +
141D ASN 3.1 18.3 + - - -
142D VAL* 3.7 9.6 - - - +
178D SER* 1.3 83.9 + - - +
180D HIS* 1.3 59.4 + - - +
181D ILE* 3.8 19.1 - - - +
198D PHE* 4.0 6.7 - - - -
199D VAL* 3.0 32.2 + - - +
201D PHE* 3.6 24.5 - - - -
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Residues in contact with HIS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ILE 4.5 7.8 + - - -
75D LEU* 4.2 23.3 - - + +
139D TYR 3.9 0.7 - - - +
140D LEU* 3.7 2.1 - - - -
141D ASN* 2.8 65.2 + - + +
179D SER* 1.3 72.3 - - - +
181D ILE* 1.3 60.5 + - - +
182D LEU* 4.2 12.3 - - + -
196D ASP* 2.6 39.2 + - + +
197D LYS 3.2 26.7 - - - -
198D PHE* 4.3 16.4 - + + -
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Residues in contact with ILE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.0 16.8 - - + +
112D CYS* 4.3 14.4 - - + -
120D LEU* 4.4 10.3 - - + -
122D CYS* 4.3 7.6 - - - -
138D LEU* 3.8 32.5 - - + -
139D TYR 3.5 1.6 - - - +
140D LEU* 3.6 36.6 - - + -
166D PHE* 5.7 0.2 - - + -
179D SER* 3.8 12.1 - - - +
180D HIS* 1.3 73.0 - - - +
182D LEU* 1.3 64.3 + - - +
196D ASP* 3.1 27.9 - - - +
197D LYS* 3.0 14.4 + - + +
199D VAL* 4.6 17.0 - - + -
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.9 9.0 - - + -
76D CYS* 3.5 31.2 - - - -
137D ASP 3.5 1.2 - - - +
138D LEU* 3.1 6.1 - - - +
139D TYR* 2.9 46.5 + - + +
141D ASN* 5.4 3.1 - - - +
147D GLN* 4.2 14.6 - - - +
180D HIS* 4.2 15.2 + - + +
181D ILE* 1.3 74.6 - - - +
183D VAL* 1.3 64.7 + - - +
184D ARG* 3.4 52.7 + - + +
194D CYS* 4.2 3.4 - - - -
195D THR 3.5 1.3 - - - +
196D ASP* 3.8 9.9 - - + +
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ALA* 3.6 29.2 + - + +
110D LEU* 3.9 25.4 - - + -
124D TRP* 4.2 15.0 - - + -
136D TYR* 3.9 24.7 - - + -
137D ASP 3.3 6.1 - - - +
138D LEU* 3.7 27.1 - - + -
182D LEU* 1.3 75.5 - - - +
184D ARG* 1.3 60.9 + - - +
193D PRO 4.6 0.3 - - - +
194D CYS* 3.5 4.0 - - - -
195D THR* 2.8 35.9 + - - +
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Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 6.0 3.4 - - - +
136D TYR* 3.4 9.1 - - - -
137D ASP* 3.0 37.6 + - + +
139D TYR* 3.8 24.8 - - + -
147D GLN* 4.5 11.5 + - - +
182D LEU* 3.4 33.3 - - + +
183D VAL* 1.3 74.8 - - - +
185D GLY* 1.3 62.8 + - - +
194D CYS* 4.0 20.9 - - + +
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLN 3.6 7.9 - - - -
136D TYR* 3.9 5.4 - - - -
183D VAL 4.1 0.6 + - - -
184D ARG* 1.3 78.4 - - - +
186D ARG* 1.3 65.6 + - - +
192D ILE* 3.5 37.9 + - - +
193D PRO 4.2 8.7 + - - -
194D CYS* 4.8 0.4 - - - +
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASP 4.1 0.9 - - - +
134D VAL* 3.5 4.0 - - - +
135D GLN* 3.1 63.7 + - + +
137D ASP* 3.1 40.1 + - - -
161D ARG* 3.9 8.3 - - - +
185D GLY* 1.3 75.3 - - - +
187D SER* 1.3 68.3 + - - +
190D PHE 5.1 0.7 - - - -
192D ILE* 3.7 9.1 - - - +
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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