Contacts of the strand formed by residues 133 - 138 (chain D) 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 SER 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLN* 3.5 30.1 + - - +
124D LEU 3.1 17.3 - - - -
125D ARG* 4.3 7.2 - - - -
130D SER 5.8 0.4 - - - -
131D ASP 3.9 4.3 + - - -
132D LYS* 1.3 77.2 - - - +
134D VAL* 1.3 67.6 + - - +
177D TRP* 4.3 8.5 - - - +
178D SER 4.8 7.1 + - - +
183D PHE* 4.5 12.0 - - - -
127E PHE* 3.8 3.9 - - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLN* 3.6 5.8 - - - +
124D LEU* 2.9 41.4 + - + -
133D SER* 1.3 77.7 - - - +
135D CYS* 1.3 66.8 + - - +
175D VAL* 4.4 9.2 - - + -
176D ALA 3.7 7.9 - - - +
177D TRP* 4.0 15.0 - - + +
185D CYS* 4.4 0.7 - - - -
127E PHE* 3.6 51.6 - - + -
143E VAL* 4.2 19.3 - - + -
145E LEU* 4.0 11.7 - - + -
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Residues in contact with CYS 135 (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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121D VAL* 4.6 0.4 - - + -
122D TYR 3.4 5.2 - - - +
134D VAL* 1.3 75.5 - - - +
136D LEU* 1.3 60.3 + - - +
137D PHE 4.2 0.4 - - - -
175D VAL* 3.4 10.0 - - - +
176D ALA* 2.7 43.2 + - + +
177D TRP* 5.2 2.7 - - - -
183D PHE* 6.4 0.4 - - - -
184D ALA 4.8 0.7 - - - -
185D CYS* 2.0 55.0 - - + -
188D ALA* 4.4 8.5 - - - -
189D PHE* 3.9 19.2 - - + -
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Residues in contact with LEU 136 (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 ALA 3.5 2.6 - - - +
121D VAL* 3.2 4.4 - - - -
122D TYR* 2.8 42.9 + - + +
124D LEU* 3.5 27.3 - - + +
135D CYS* 1.3 74.0 - - - +
137D PHE* 1.3 57.6 + - - +
138D THR* 3.8 19.2 + - + -
173D SER* 3.8 23.8 - - - -
174D ALA 3.8 12.6 - - - +
175D VAL* 4.2 5.4 - - + -
189D PHE* 4.3 2.9 - - - -
133E GLU* 4.4 6.5 - - - +
141E THR* 3.6 33.7 - - + +
143E VAL* 4.3 4.0 - - + -
192E ARG* 4.0 19.1 - - + -
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Residues in contact with PHE 137 (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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119D PRO* 4.3 18.8 - - + -
120D ALA* 3.7 11.9 - - - -
121D VAL* 4.0 13.7 - - + +
136D LEU* 1.3 71.4 - - - +
138D THR* 1.3 62.5 + - - +
140D PHE* 3.3 44.3 - + + -
144D THR* 4.3 11.9 - - + -
146D VAL* 4.3 9.0 - - + -
173D SER* 3.0 5.4 - - - -
174D ALA* 2.8 38.2 + - + +
189D PHE* 3.5 49.1 - + + -
192D SER* 4.1 26.0 - - - -
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Residues in contact with THR 138 (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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119D PRO* 3.6 0.7 - - - +
120D ALA 3.1 26.5 + - - -
122D TYR* 3.6 35.0 - - + -
136D LEU* 4.1 14.8 - - + -
137D PHE* 1.3 75.8 - - - +
139D ASP* 1.3 92.4 + - - +
140D PHE* 3.3 7.1 + - - -
171D SER* 4.4 2.1 + - - -
172D ASN 3.1 12.9 + - - -
173D SER* 4.0 9.7 - - - -
133E GLU* 4.9 0.9 - - - +
141E THR* 5.1 1.1 + - - -
194E ARG* 4.0 13.7 + - - +
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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