Contacts of the strand formed by residues 144 - 148 (chain A) 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 ARG 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 4.1 0.2 - - - +
138A SER* 3.5 2.1 - - - -
139A THR* 2.9 42.3 + - - +
140A ASP* 5.6 0.4 - - - +
142A PHE 3.2 0.2 - - - -
143A THR* 1.3 87.6 + - + +
145A ILE* 1.3 67.3 + - - +
146A LEU* 3.6 32.4 + - + +
201A ALA* 4.0 23.6 + - + +
204A TYR* 3.8 22.8 + - - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 6.1 1.3 - - + -
71A GLU 3.3 26.5 - - - +
72A PHE* 3.3 31.6 - - + +
136A TYR* 4.1 15.4 - - + -
137A LEU 3.4 6.7 - - - +
138A SER* 3.9 17.3 - - - -
142A PHE* 5.0 16.6 - - + +
144A ARG* 1.3 83.6 + - - +
146A LEU* 1.3 64.5 + - - +
147A GLU 4.2 0.2 + - - -
204A TYR* 3.7 17.0 + - - -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 3.3 5.1 - - - -
137A LEU* 2.5 64.0 + - + +
139A THR* 4.5 15.0 - - + +
144A ARG* 3.6 49.8 - - + +
145A ILE* 1.3 73.4 - - - +
147A GLU* 1.3 60.7 + - - +
197A GLN 4.5 2.2 - - - +
200A ILE* 3.7 28.9 - - + -
201A ALA* 3.7 21.8 - - + +
204A TYR* 3.7 15.9 - - + -
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ARG* 2.7 29.6 + - - +
94A GLU* 4.6 1.2 - - - +
96A LYS* 5.8 0.9 - - - -
119A TYR* 4.5 2.8 - - - -
134A THR* 2.9 35.5 + - - +
135A CYS 3.4 7.4 - - - +
136A TYR* 3.4 36.0 + - + +
145A ILE 4.2 0.2 + - - -
146A LEU* 1.3 73.3 - - - +
148A TYR* 1.3 60.8 + - - +
149A ALA 4.3 0.2 - - - -
152A ARG* 2.8 32.7 + - - -
200A ILE* 4.6 3.3 - - - +
204A TYR* 3.4 40.8 + - + +
211A ASN* 5.2 2.3 + - - -
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 5.2 2.2 - - + -
135A CYS* 3.0 46.8 + - + +
137A LEU* 5.6 4.3 - - + +
146A LEU 3.9 2.4 + - - +
147A GLU* 1.3 75.6 - - - +
149A ALA* 1.3 63.0 + - - +
150A PRO* 3.6 20.2 - - + +
178A VAL* 4.0 19.5 - - + -
180A LEU* 3.8 22.4 - - + -
193A LEU 4.4 1.6 + - - -
194A SER* 4.0 5.7 + - - -
195A ALA* 3.7 19.4 + - + +
200A ILE* 3.8 41.1 - - + -
213A VAL* 3.8 21.8 - - + -
216A GLN* 2.7 33.0 + - - -
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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