Contacts of the strand formed by residues 123 - 130 (chain D) in PDB entry 3VI4
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 ILE 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.6 4.9 + - + +
122D PRO* 1.3 80.6 - - - +
124D ASP* 1.3 65.1 + - - +
153D MET* 3.9 22.2 - - + -
156D ILE* 4.5 6.3 - - + +
157D THR* 3.7 22.2 + - + -
159D ASP 2.8 10.0 + - - +
160D PHE* 3.4 27.6 - - + -
161D ARG 2.8 31.7 + - - -
248D ARG* 3.7 5.0 + - - -
251D THR* 3.4 17.3 - - + +
253D LEU* 4.2 13.5 - - + -
355D TYR* 4.2 26.2 - - + +
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Residues in contact with ASP 124 (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 ILE* 1.3 73.9 - - - +
125D LEU* 1.3 60.5 + - - +
161D ARG* 3.3 19.0 - - - +
205D LEU* 3.5 12.5 - - + +
246D GLY 3.7 1.2 - - - +
247D TRP* 3.4 27.2 - - + -
248D ARG* 2.8 61.4 + - - +
250D VAL* 3.9 5.5 - - + +
251D THR 3.0 11.1 + - - +
252D ARG* 3.3 2.2 - - + -
253D LEU 2.8 24.9 + - - -
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Residues in contact with LEU 125 (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 ILE* 3.9 1.1 - - + -
124D ASP* 1.3 75.0 - - - +
126D TYR* 1.3 74.2 + - - +
127D TYR* 3.7 10.1 - - + +
149D LEU* 4.2 18.8 - - + -
153D MET* 5.2 1.6 - - + -
160D PHE* 3.7 22.7 - - + -
161D ARG 3.1 9.3 + - - +
162D ILE* 3.6 20.7 - - + -
163D GLY 2.9 24.4 + - - -
205D LEU* 3.4 3.9 - - - +
253D LEU* 3.3 25.8 - - + +
255D VAL* 3.7 28.3 - - + -
351D ILE* 4.3 11.2 - - + -
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Residues in contact with TYR 126 (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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125D LEU* 1.3 75.2 - - - +
127D TYR* 1.3 63.7 + - - +
128D LEU* 4.0 7.0 - - + -
163D GLY* 3.8 12.6 - - - -
164D PHE 2.9 12.1 + - - -
165D GLY* 3.0 31.0 - - - -
199D TYR* 3.1 13.2 + - - -
201D ASN* 2.7 29.7 + - - -
203D LEU 3.7 11.7 - - - -
204D SER* 5.1 1.6 - - - -
205D LEU* 4.7 3.4 - - + -
238D VAL* 3.8 28.0 - - + -
245D ILE* 3.9 25.4 - - + -
247D TRP* 3.4 23.9 - - + -
253D LEU 2.7 11.1 + - - +
254D LEU* 3.4 9.9 - - + +
255D VAL 2.8 25.8 + - - -
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Residues in contact with TYR 127 (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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125D LEU* 3.7 10.4 - - + +
126D TYR* 1.3 72.6 - - - +
128D LEU* 1.3 58.4 + - - +
129D MET* 3.8 30.4 - - + -
142D VAL* 4.4 8.9 - - + +
145D LEU* 4.3 21.3 - - + -
149D LEU* 5.5 3.4 - - + -
162D ILE* 5.8 0.2 - - + -
163D GLY 3.1 17.9 + - - +
164D PHE* 3.3 23.6 - + + -
165D GLY 2.8 26.5 + - - +
212D PHE* 4.3 11.0 - + + -
255D VAL* 3.7 33.9 - - + -
257D SER* 3.4 17.8 + - - -
344D SER* 4.4 1.9 + - - -
347D VAL* 3.4 25.6 - - + +
351D ILE* 4.3 13.5 - - + -
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Residues in contact with LEU 128 (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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126D TYR* 3.5 5.9 + - + -
127D TYR* 1.3 72.2 - - - +
129D MET* 1.3 60.1 + - - +
165D GLY* 3.3 24.5 - - - +
166D SER 4.0 0.7 - - - +
167D PHE* 3.8 21.5 - - + -
199D TYR* 3.9 20.2 - - + -
234D ALA* 3.6 24.5 - - + -
235D ILE* 3.7 17.5 - - - +
238D VAL* 3.9 11.7 - - + -
254D LEU* 3.7 21.8 - - + -
255D VAL 2.9 18.4 + - - +
256D PHE* 3.6 13.9 - - + -
257D SER* 3.1 17.3 + - - +
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Residues in contact with MET 129 (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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127D TYR* 3.8 26.7 - - + -
128D LEU* 1.3 74.5 - - - +
130D ASP* 1.3 74.4 + - - +
131D LEU* 3.3 5.9 + - + +
135D MET* 3.9 12.1 - - + +
138D ASP* 3.6 21.3 - - + +
139D LEU* 3.6 35.9 - - + +
142D VAL* 4.4 15.3 - - + -
164D PHE* 4.1 19.5 - - + -
165D GLY 2.7 14.3 + - - +
166D SER* 3.3 6.6 - - - -
167D PHE* 3.1 25.5 + - - -
257D SER* 3.7 14.6 - - - +
344D SER* 5.0 1.3 - - - +
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Residues in contact with ASP 130 (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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129D MET* 1.3 77.2 - - - +
131D LEU* 1.3 64.3 + - - +
132D SER* 2.7 49.3 + - - -
135D MET* 3.3 29.4 - - + +
167D PHE* 3.7 24.7 - - + +
168D VAL* 5.1 0.2 - - - -
229D GLU* 3.5 11.3 - - - +
257D SER 3.0 20.0 + - - +
258D THR* 2.9 30.6 + - - -
259D ASP* 4.0 2.1 + - - +
260D ALA 4.7 0.2 + - - -
502D MG 3.6 3.3 - - - -
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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