Contacts of the strand formed by residues 139 - 149 (chain E) in PDB entry 3VXR
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 LYS 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D MET* 3.9 16.6 - - + -
167D MET* 4.0 20.1 - - - -
169D PHE* 3.7 55.6 - - + -
133E GLU* 3.4 18.3 - - - +
134E ILE* 3.6 13.2 + - - -
137E THR* 3.1 24.4 + - - +
138E GLN* 1.3 84.6 + - - +
140E ALA* 1.3 61.4 + - - +
194E ARG* 3.5 20.2 - - - +
195E VAL 3.5 11.2 - - - +
196E SER* 5.1 1.3 - - - -
197E ALA* 3.9 1.6 - - - +
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PRO* 3.7 22.2 - - + -
133E GLU* 3.8 2.9 - - - -
134E ILE* 4.2 8.1 - - + -
139E LYS* 1.3 75.5 - - - +
141E THR* 1.3 62.3 + - - +
142E LEU* 3.9 1.0 + - - +
193E LEU 3.6 1.4 - - - +
194E ARG* 3.3 3.0 - - - -
195E VAL* 2.8 42.4 + - + +
196E SER 4.4 2.7 - - - +
197E ALA* 4.5 2.0 - - - -
200E TRP* 3.7 27.4 - - + -
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.4 10.9 - - - +
136D LEU* 3.6 20.9 - - + +
138D THR* 5.1 1.7 + - - -
162D LEU* 5.0 2.9 - - + +
173D SER* 5.9 1.1 - - - +
129E PRO* 3.4 22.6 - - - +
133E GLU* 2.6 32.8 + - - +
140E ALA* 1.3 71.6 - - - +
142E LEU* 1.3 73.0 + - - +
143E VAL* 4.7 0.4 - - + -
192E ARG* 3.7 26.9 - - + -
193E LEU 3.5 7.9 - - - +
194E ARG* 3.1 21.2 + - + +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 4.3 17.0 - - + -
127E PHE 3.5 8.3 - - - +
128E GLU* 5.0 0.2 - - - -
129E PRO* 3.7 17.7 - - + -
140E ALA 4.3 6.7 - - - +
141E THR* 1.3 75.6 - - - +
143E VAL* 1.3 61.2 + - - +
158E TRP* 3.9 15.2 - - + -
191E SER 3.8 0.2 - - - +
192E ARG* 3.2 5.0 - - - -
193E LEU* 2.7 60.6 + - + +
195E VAL* 4.7 5.6 - - + -
200E TRP* 4.0 17.9 - - + -
207E PHE* 3.9 48.2 - - + -
238E ALA* 4.4 3.6 - - + -
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.8 17.2 - - + +
134D VAL* 4.2 21.8 - - + -
136D LEU* 4.3 11.2 - - + -
175D VAL* 4.1 33.7 - - + -
126E VAL* 3.6 3.3 - - - +
127E PHE* 2.8 41.1 + - + +
141E THR* 4.7 1.3 - - + -
142E LEU* 1.3 75.6 - - - +
144E CYS* 1.3 71.0 + - - +
145E LEU* 4.7 2.0 - - + +
158E TRP* 4.1 2.5 - - - -
190E SER* 4.6 2.2 - - - -
191E SER 3.2 7.4 - - - +
192E ARG* 3.8 18.6 - - + -
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Residues in contact with CYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 3.8 11.9 - - - -
125E ALA 3.5 9.6 - - - -
126E VAL* 4.6 0.4 - - + +
143E VAL* 1.3 73.8 - - - +
145E LEU* 1.3 65.2 + - - +
156E LEU* 4.2 8.9 - - - +
158E TRP* 3.4 18.3 - - + -
189E LEU 3.8 0.6 - - - +
190E SER* 3.1 8.1 - - - -
191E SER* 2.6 39.5 + - - +
209E CYS* 2.0 51.1 - - + -
211E VAL* 4.6 1.1 - - - -
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Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 4.0 14.4 - - + -
175D VAL* 4.9 3.6 - - + -
177D TRP* 3.5 66.0 - - + +
123E GLU 3.5 1.7 - - - +
124E VAL* 3.3 4.4 - - - +
125E ALA* 2.9 38.1 + - + +
127E PHE* 3.8 22.2 - - + -
143E VAL* 4.2 1.5 - - + -
144E CYS* 1.3 76.9 - - - +
146E ALA* 1.3 60.9 + - - +
147E THR* 3.8 17.1 - - + +
189E LEU 3.6 5.2 - - - +
190E SER* 3.8 18.6 - - - -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E PRO* 4.1 11.2 - - + -
123E GLU 3.2 5.4 - - - +
124E VAL* 4.4 1.1 - - + +
144E CYS* 4.3 0.4 - - - -
145E LEU* 1.3 72.3 - - - +
147E THR* 1.3 61.5 + - - +
149E PHE* 3.5 16.0 - - + -
156E LEU* 5.1 2.0 - - + -
188E ALA* 3.1 6.6 - - - +
189E LEU* 2.8 48.2 + - + +
211E VAL* 4.0 28.9 - - + -
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Residues in contact with THR 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TRP* 4.5 8.1 - - - +
122E PRO* 3.3 2.3 - - - +
123E GLU* 2.8 53.7 + - - +
145E LEU* 3.8 30.1 - - + +
146E ALA* 1.3 80.0 - - - +
148E GLY* 1.3 64.6 + - - +
149E PHE* 3.3 4.8 + - - -
178E GLU* 3.5 13.0 - - - +
187E TYR 3.6 2.0 - - - -
188E ALA* 4.3 6.3 - - + +
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Residues in contact with GLY 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E PHE* 3.6 8.7 - - - +
121E PRO 3.5 10.5 - - - +
123E GLU* 5.8 2.2 - - - -
147E THR* 1.3 72.2 - - - +
149E PHE* 1.3 58.7 + - - +
178E GLU* 2.8 28.6 + - - -
186E ARG* 3.3 33.6 + - - -
187E TYR 3.0 3.9 + - - -
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Residues in contact with PHE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E PHE 3.1 16.6 - - - +
121E PRO 4.0 0.2 - - - -
122E PRO* 3.6 34.5 - - + -
146E ALA* 3.5 26.7 - - + -
147E THR 3.3 1.1 + - - -
148E GLY* 1.3 78.2 - - - +
150E TYR* 1.3 57.2 + - - +
151E PRO 3.4 15.0 - - - -
152E ASP* 4.1 10.3 - - - -
154E VAL* 3.7 39.7 - - + -
175E PRO* 4.1 6.1 - - + -
186E ARG* 4.1 0.7 - - - -
187E TYR* 2.6 68.9 + - + -
188E ALA* 3.9 2.7 - - - -
189E LEU* 4.0 12.3 - - + -
213E PHE* 4.1 4.0 - - + -
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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