Contacts of the strand formed by residues 140 - 147 (chain D) in PDB entry 4H0N
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 PHE 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D LEU* 3.9 21.1 - - + -
111D VAL* 3.2 26.7 - - + -
112D ASP 3.8 12.3 - - - -
114D ILE* 3.9 22.9 - - + -
135D LEU* 2.6 44.5 + - + +
136D LYS* 4.3 7.3 - - - +
138D CYS* 3.9 18.6 - - + -
139D ASN* 1.3 74.3 - - - +
141D ILE* 1.3 66.6 + - - +
142D TYR* 4.3 6.9 - - - -
165D ALA* 3.9 7.4 - - + -
166D ARG* 3.3 28.5 - - - -
167D ARG* 3.5 34.8 - - - -
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Residues in contact with ILE 141 (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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139D ASN 4.3 0.4 + - - -
140D PHE* 1.3 74.9 - - - +
142D TYR* 1.3 62.9 + - - +
165D ALA* 3.2 2.3 - - - -
166D ARG* 2.7 46.0 + - + +
167D ARG 4.7 1.3 - - - +
168D ASN* 3.6 37.9 - - - +
170D LEU* 6.1 2.5 - - - +
172D TRP* 3.6 42.4 - - + +
174D PHE 5.9 0.4 - - - +
176D ARG* 4.8 17.7 - - + +
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Residues in contact with TYR 142 (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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128D ARG* 4.6 4.3 + - - -
132D ILE* 3.6 38.0 - - + +
135D LEU* 3.9 19.1 - - + -
136D LYS* 3.6 31.3 + - + -
140D PHE 4.3 5.2 - - - -
141D ILE* 1.3 83.0 - - - +
143D GLN* 1.3 62.9 + - - +
144D GLU* 4.1 26.5 - - + -
163D CYS* 4.1 3.8 - - - -
164D THR 3.1 12.1 - - - +
165D ALA* 3.9 12.3 - - + -
172D TRP* 4.4 6.4 - - - -
176D ARG* 2.8 53.0 + - - +
178D ASP* 4.4 11.8 + - - -
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Residues in contact with GLN 143 (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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142D TYR* 1.3 75.6 - - - +
144D GLU* 1.3 84.4 + - - +
145D PHE* 3.4 26.3 - - + -
163D CYS* 3.3 3.6 - - - -
164D THR* 2.8 43.5 + - - +
172D TRP* 4.2 5.2 - - + -
174D PHE* 3.7 14.2 - - + -
176D ARG* 3.2 8.2 - - + +
177D ARG* 2.7 48.4 + - - +
178D ASP 5.0 0.2 - - - -
179D GLU 3.2 18.2 + - - -
181D ILE* 3.5 16.7 - - + +
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Residues in contact with GLU 144 (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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123D GLU* 5.3 0.4 - - - -
128D ARG* 3.0 41.1 + - - -
132D ILE* 3.5 7.1 - - - +
142D TYR* 4.1 18.3 - - + -
143D GLN* 1.3 89.8 + - - +
145D PHE* 1.3 63.4 + - - +
161D TYR* 2.7 35.8 + - + +
162D TYR 3.2 6.7 - - - +
163D CYS* 4.5 3.4 - - + -
177D ARG 5.2 0.2 + - - -
178D ASP 4.7 6.6 - - - +
180D ILE* 3.5 30.1 - - + +
181D ILE 3.0 22.2 + - - -
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Residues in contact with PHE 145 (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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143D GLN* 3.4 28.0 - - + -
144D GLU* 1.3 74.9 - - - +
146D LEU* 1.3 64.5 + - - +
147D LEU* 3.7 26.7 - - + -
161D TYR* 3.3 5.6 - - - -
162D TYR* 2.6 56.3 + - + +
164D THR* 3.3 33.9 - - + -
172D TRP* 6.3 0.2 - + - -
174D PHE* 4.4 11.4 - + - -
180D ILE* 4.0 1.6 - - - -
181D ILE* 3.3 47.6 - - + +
184D LEU* 4.2 14.4 - - + -
185D PRO* 6.1 1.3 - - + -
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Residues in contact with LEU 146 (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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120D LYS* 4.2 21.1 - - + -
123D GLU* 3.6 39.0 - - + +
145D PHE* 1.3 71.5 - - - +
147D LEU* 1.3 60.8 + - - +
148D CYS 4.4 0.2 + - - -
159D LEU* 3.9 15.4 - - + +
160D ARG 3.3 3.1 - - - +
161D TYR* 3.6 30.5 - - + +
180D ILE* 3.5 25.0 - - + +
181D ILE 3.0 6.3 + - - -
182D THR* 3.3 33.6 - - + +
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Residues in contact with LEU 147 (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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145D PHE* 3.7 23.8 - - + -
146D LEU* 1.3 75.8 - - - +
148D CYS* 1.3 62.7 + - - +
149D PRO* 4.0 1.9 - - - +
151D THR* 5.0 5.2 - - - +
158D ARG 3.6 4.3 - - - +
159D LEU* 3.7 4.9 - - - +
160D ARG 3.0 27.0 + - - +
162D TYR* 4.0 24.2 + - + -
181D ILE 3.9 5.2 - - - +
182D THR 3.2 31.4 - - - +
183D ARG* 3.8 14.6 - - - +
184D LEU* 3.7 32.3 - - + +
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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