Contacts of the strand formed by residues 143 - 150 (chain A) in PDB entry 6TAV
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 THR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ASP* 4.0 4.2 - - - +
138A TYR* 4.7 1.1 - - - -
141A GLY 4.9 3.1 - - - +
142A GLN* 1.3 90.1 + - - +
144A VAL* 1.3 61.6 + - - +
145A LYS* 3.7 23.1 + - - +
191A SER* 4.6 11.2 - - - +
192A PHE 3.6 7.6 - - - -
193A PRO* 3.6 28.9 - - + -
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Residues in contact with VAL 144 (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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133A THR* 4.6 6.7 - - + -
138A TYR* 3.6 35.7 - - + +
142A GLN 3.9 2.0 + - - -
143A THR* 1.3 71.8 - - - +
145A LYS* 1.3 67.2 + - - +
146A PHE* 4.4 9.1 + - + -
167A ILE* 4.3 7.0 - - + -
191A SER* 3.3 4.3 - - - -
192A PHE* 2.8 73.8 + - + +
194A LEU* 4.2 15.0 - - + +
219A PHE* 4.6 19.3 - - + -
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Residues in contact with LYS 145 (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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133A THR* 3.5 2.6 - - - +
134A ASP* 2.8 54.8 + - + +
138A TYR* 3.8 1.9 + - - -
143A THR* 4.0 22.9 - - - +
144A VAL* 1.3 77.1 - - - +
146A PHE* 1.3 58.7 + - - +
190A PHE 3.5 11.9 - - - +
191A SER* 4.7 9.6 - - - -
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Residues in contact with PHE 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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131A VAL* 3.9 21.3 - - + -
132A GLN 3.2 14.6 - - - +
133A THR* 3.7 15.9 - - + -
134A ASP 4.9 0.2 - - - +
144A VAL* 4.7 9.6 - - + -
145A LYS* 1.3 76.1 - - - +
147A ARG* 1.3 61.7 + - - +
148A VAL* 4.8 2.2 - - + -
165A VAL* 4.3 8.7 - - + -
167A ILE* 4.0 14.1 - - + -
178A TRP* 3.6 37.2 - + - -
189A GLN* 3.5 2.3 - - - +
190A PHE* 2.7 77.1 + + + +
191A SER* 4.6 2.0 - - - -
205A VAL* 3.9 22.0 - - + -
219A PHE* 6.4 0.2 - + - -
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Residues in contact with ARG 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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130A PHE 4.1 0.3 - - - +
131A VAL* 3.3 5.6 - - - -
132A GLN* 2.7 79.0 + - + +
146A PHE* 1.3 77.1 - - - +
148A VAL* 1.4 58.9 + - - +
149A VAL* 4.7 4.4 - - + +
187A LEU* 3.8 20.9 - - + -
188A LYS 3.5 5.6 - - - -
189A GLN* 3.3 42.9 + - + +
596A ALA* 3.6 28.1 - - - +
597A LEU 3.2 30.3 + - - +
598A ARG* 4.3 5.3 - - - +
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Residues in contact with VAL 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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129A VAL* 3.8 22.9 - - + -
130A PHE 3.5 7.9 - - - +
131A VAL* 3.6 17.5 - - + -
146A PHE* 4.6 3.3 - - + -
147A ARG* 1.4 69.8 - - - +
149A VAL* 1.3 67.3 + - - +
162A ILE* 5.1 9.0 - - + -
165A VAL* 5.5 4.5 - - + -
183A LEU* 3.3 18.4 - - + +
187A LEU* 3.1 4.0 - - - +
188A LYS 3.0 37.4 + - - +
190A PHE* 3.7 22.0 - - + -
207A VAL* 4.2 17.3 - - + -
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Residues in contact with VAL 149 (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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129A VAL* 2.9 25.4 - - - +
130A PHE* 3.0 65.2 + - + +
147A ARG* 4.7 5.2 - - + +
148A VAL* 1.3 78.8 - - - +
150A SER* 1.4 62.2 + - - +
151A MET* 4.3 12.6 - - + -
157A PRO* 6.4 0.2 - - + -
183A LEU* 4.4 2.7 - - - -
186A GLY 3.3 19.1 - - - +
187A LEU* 4.0 15.0 - - + -
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Residues in contact with SER 150 (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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127A SER* 2.9 32.9 + - - -
128A LEU 3.6 6.5 - - - -
129A VAL* 4.2 9.0 - - - -
149A VAL* 1.4 75.6 - - - +
151A MET* 1.4 63.0 + - - +
157A PRO* 4.0 0.7 - - - +
158A LEU* 3.0 30.7 + - - +
160A GLU* 3.9 10.6 + - - +
183A LEU* 3.4 23.2 - - - +
186A GLY 3.5 8.5 + - - +
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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