Contacts of the strand formed by residues 160 - 167 (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 PHE 160 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 3.5 24.2 - - + -
125D LEU* 3.7 19.7 - - + -
149D LEU* 3.9 11.0 - - + -
150D MET* 3.9 34.8 - - + +
153D MET* 3.5 44.0 - - + -
154D ARG* 4.5 10.9 - - + +
157D THR* 3.6 12.7 + - + +
158D SER 4.2 0.8 - - - -
159D ASP* 1.3 76.2 + - - +
161D ARG* 1.3 82.5 + - - +
162D ILE* 3.3 35.2 - - + -
207D ASN* 3.9 17.5 - - - +
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Residues in contact with ARG 161 (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 2.8 9.2 + - - +
124D ASP* 3.3 21.5 + - - +
125D LEU 3.1 22.2 + - - +
150D MET* 5.5 0.2 - - - -
159D ASP* 4.9 2.7 + - - +
160D PHE* 1.3 90.2 - - - +
162D ILE* 1.3 64.7 + - - +
205D LEU* 3.5 38.7 + - + +
206D THR* 3.2 12.6 - - - +
207D ASN* 4.2 8.4 - - + +
246D GLY* 2.9 27.3 + - - -
248D ARG* 2.8 46.7 - - - +
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Residues in contact with ILE 162 (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* 3.6 10.3 - - + -
127D TYR* 5.8 0.2 - - + -
146D GLY* 4.7 13.5 - - - +
149D LEU* 3.6 27.4 - - + -
150D MET* 4.8 5.1 - - + +
160D PHE* 3.3 35.2 - - + -
161D ARG* 1.3 72.5 - - - +
163D GLY* 1.3 63.4 + - - +
203D LEU* 4.3 1.0 - - - +
204D SER 3.4 4.0 - - - +
205D LEU* 3.8 4.5 - - - -
206D THR* 2.7 40.7 + - + +
208D LYS 5.7 0.4 - - - +
209D GLY* 5.6 3.8 - - - +
212D PHE* 2.8 49.6 - - + -
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Residues in contact with GLY 163 (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 2.9 10.1 + - - +
126D TYR* 3.8 16.2 - - - -
127D TYR* 3.1 24.1 + - - +
162D ILE* 1.3 86.3 - - - +
164D PHE* 1.3 61.6 + - - +
203D LEU* 3.4 13.5 - - - -
204D SER 3.9 3.8 - - - -
205D LEU* 3.4 5.2 - - - +
212D PHE* 4.4 0.2 - - - -
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Residues in contact with PHE 164 (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* 2.9 11.2 + - - -
127D TYR* 3.3 39.5 - + - -
129D MET* 4.1 22.2 - - + -
131D LEU* 5.2 2.2 - - + -
139D LEU* 4.9 6.5 - - + -
142D VAL* 4.6 1.1 - - + -
163D GLY* 1.3 74.8 - - - +
165D GLY* 1.3 70.1 + - - +
166D SER* 4.4 7.6 - - - -
202D VAL* 3.1 38.3 + - + -
203D LEU* 2.9 41.0 + - + +
212D PHE* 3.6 26.7 - + + +
216D VAL* 3.7 30.5 - - + -
219D GLN* 4.5 6.3 - - + -
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Residues in contact with GLY 165 (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* 3.0 21.6 + - - -
127D TYR 2.8 9.1 + - - +
128D LEU* 3.3 8.8 - - - -
129D MET* 2.7 31.7 + - - -
164D PHE* 1.3 83.3 - - - +
166D SER* 1.3 56.2 + - - -
199D TYR* 4.2 0.2 - - - -
200D LYS 3.3 8.3 - - - -
202D VAL 4.0 0.2 - - - -
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Residues in contact with SER 166 (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 LEU* 4.3 2.0 - - - -
129D MET 3.3 4.5 - - - -
131D LEU* 3.3 34.6 - - - +
164D PHE* 4.4 8.3 - - - -
165D GLY* 1.3 74.0 - - - -
167D PHE* 1.3 60.6 + - - +
197D PHE* 3.4 20.8 - - - -
199D TYR* 3.3 5.5 - - - -
200D LYS* 2.7 52.5 + - - +
202D VAL* 3.9 7.6 - - - +
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.8 21.3 - - + -
129D MET 3.1 10.2 + - - -
130D ASP* 3.7 35.8 - - + +
131D LEU* 2.9 25.6 + - - -
166D SER* 1.3 75.9 - - - +
168D VAL* 1.3 72.9 + - - +
197D PHE* 4.5 2.0 - - - -
198D SER 3.2 13.2 - - - +
229D GLU* 3.8 17.5 - - + -
230D GLY 4.2 2.0 - - - +
231D GLY* 3.7 26.7 - - - -
234D ALA* 3.6 17.9 - - + -
256D PHE* 3.2 40.8 - + - -
257D SER 4.4 1.3 - - - -
258D THR* 4.1 6.7 - - + -
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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