Contacts of the strand formed by residues 155 - 165 (chain D) in PDB entry 1VBF
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 LEU 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D PRO* 5.4 0.2 - - - -
135D TYR* 3.2 22.0 - - - +
136D ASP 3.5 21.8 - - - +
137D ARG 4.1 1.1 - - - +
138D VAL* 4.1 17.7 - - + -
151D PRO 3.1 7.3 + - - +
152D TYR* 3.4 20.0 - - + +
153D GLU 3.0 4.3 - - - +
154D GLN* 1.3 78.0 - - - +
156D LYS* 1.3 63.6 + - - +
159D GLY* 3.4 31.6 - - - +
160D ILE 3.8 15.5 - - - +
161D MSE 4.1 11.2 - - + +
176D VAL 4.6 0.4 - - - +
178D LYS* 3.0 36.7 + - + +
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Residues in contact with LYS 156 (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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72D GLN* 5.2 1.8 - - - +
134D PRO* 5.2 9.9 - - + -
135D TYR 2.8 22.5 + - - +
136D ASP* 2.5 53.6 + - - +
137D ARG* 4.4 13.5 - - - +
154D GLN 3.8 0.8 + - - -
155D LEU* 1.3 77.3 - - - +
157D GLU* 1.3 66.4 + - - +
158D GLY* 4.1 6.1 - - - +
159D GLY* 2.9 28.9 + - - +
178D LYS* 3.4 7.0 - - - +
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Residues in contact with GLU 157 (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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155D LEU 3.8 0.4 + - - -
156D LYS* 1.3 75.0 - - - +
158D GLY* 1.3 57.3 + - - +
178D LYS* 2.6 48.8 - - - +
179D LYS* 3.4 8.1 - - - -
180D GLY* 2.9 31.9 + - - -
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Residues in contact with GLY 158 (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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137D ARG* 5.3 2.1 + - - -
156D LYS* 3.4 10.4 - - - +
157D GLU* 1.3 77.8 - - - +
159D GLY* 1.3 67.6 + - - +
160D ILE* 3.8 6.1 + - - +
177D ILE* 3.9 12.2 - - - +
178D LYS 4.3 3.8 - - - -
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Residues in contact with GLY 159 (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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136D ASP 3.4 15.3 - - - -
137D ARG* 4.6 0.4 - - - -
155D LEU* 3.4 12.7 - - - +
156D LYS* 2.9 28.5 + - - +
157D GLU 3.1 0.6 - - - -
158D GLY* 1.3 83.7 - - - +
160D ILE* 1.3 60.6 + - - -
177D ILE* 3.5 2.8 - - - -
178D LYS 3.0 24.8 + - - -
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Residues in contact with ILE 160 (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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65D GLU 4.7 0.9 - - - +
66D LEU* 4.1 12.8 - - + +
67D ASP* 4.2 12.1 - - + +
136D ASP 3.2 5.7 + - - -
137D ARG* 3.3 42.9 - - - +
138D VAL 3.2 19.9 + - - -
155D LEU* 3.8 3.9 - - - +
158D GLY 4.2 6.5 - - - +
159D GLY* 1.3 77.3 - - - +
161D MSE 1.3 73.3 + - - +
162D ILE* 4.4 6.3 - - + -
175D LYS* 4.1 31.6 - - + +
176D VAL 3.4 6.3 - - - +
177D ILE* 4.4 15.3 - - + -
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Residues in contact with MSE 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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138D VAL* 3.2 31.0 - - + +
140D VAL* 3.5 21.3 - - + -
147D LEU* 4.3 24.2 - - - -
148D LEU* 4.4 7.4 - - + +
151D PRO* 3.1 37.9 - - + +
152D TYR* 4.4 11.4 - - + -
155D LEU* 4.1 11.9 - - + -
160D ILE* 1.3 75.9 - - - +
162D ILE* 1.3 79.3 + - - +
163D LEU* 4.3 8.5 - - + -
175D LYS* 3.5 0.3 - - - -
176D VAL* 2.7 47.8 + - + +
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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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62D MSE 3.9 19.3 - - + +
65D GLU* 3.3 46.2 - - + +
66D LEU* 3.8 7.4 - - + +
138D VAL 3.1 7.7 + - - +
139D VAL* 3.6 12.1 - - + +
140D VAL* 3.1 25.1 + - - +
160D ILE* 4.4 5.4 - - + -
161D MSE 1.3 85.4 - - - +
163D LEU* 1.3 62.5 + - - +
173D LEU* 3.8 27.1 - - + -
174D TYR 3.3 5.2 - - - +
175D LYS* 4.1 18.2 - - + -
188D LEU* 4.3 4.5 - - + -
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Residues in contact with LEU 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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140D VAL* 3.5 18.2 - - + -
142D ALA 5.1 0.4 - - - +
144D ALA* 4.9 1.3 - - + -
146D THR 4.5 1.8 - - - +
147D LEU* 4.4 4.5 - - + -
148D LEU* 4.0 41.5 - - + +
161D MSE 4.3 10.3 - - - -
162D ILE* 1.3 76.8 - - - +
164D PRO* 1.3 75.7 - - + +
165D ILE* 3.5 33.9 - - + -
173D LEU* 3.4 6.7 - - - +
174D TYR* 2.8 39.5 + - + +
176D VAL* 4.3 11.9 - - + -
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Residues in contact with PRO 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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140D VAL 3.6 12.6 - - - +
142D ALA 3.2 21.9 - - - +
143D THR* 3.3 19.1 - - + -
144D ALA 3.1 18.5 + - - -
163D LEU* 1.3 91.9 - - + +
165D ILE* 1.3 62.3 + - - +
172D LYS 3.2 12.1 - - - +
173D LEU* 4.2 4.5 - - + -
191D VAL* 3.9 7.4 - - + -
193D PHE* 3.7 39.9 - - + -
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Residues in contact with ILE 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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203C TYR* 4.2 26.5 - - + +
204C ASP* 5.4 0.5 - - - -
143D THR* 4.4 0.2 - - - -
144D ALA 3.4 12.1 - - - +
145D PRO 3.8 4.0 - - - +
146D THR* 3.5 22.0 - - - +
147D LEU* 4.0 26.5 - - + +
163D LEU* 3.5 31.9 - - + -
164D PRO* 1.3 76.8 - - - +
166D GLY* 1.3 62.5 + - - +
171D GLN* 3.3 15.1 - - - +
172D LYS* 2.9 19.1 + - - +
174D TYR* 3.6 31.2 - - + -
176D VAL* 5.5 0.2 - - + -
185D LEU* 5.1 2.5 - - + -
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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