Contacts of the strand formed by residues 129 - 133 (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 VAL 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A SER* 4.1 3.1 - - - +
128A LEU* 1.3 74.1 - - - +
130A PHE* 1.4 61.0 + - - +
148A VAL* 3.8 19.5 - - + -
149A VAL 2.9 26.9 - - - +
150A SER* 4.2 11.0 - - - +
151A MET* 4.6 1.3 - - - -
160A GLU* 5.4 0.2 - - - +
162A ILE* 5.2 6.7 - - + -
207A VAL* 4.2 12.3 - - + -
209A LYS* 3.4 24.5 - - + +
215A THR* 3.1 43.6 - - - +
621A LEU* 3.2 19.6 - - - +
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Residues in contact with PHE 130 (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* 1.4 75.7 - - - +
131A VAL* 1.4 74.9 + - - +
132A GLN* 4.7 7.6 - - + -
147A ARG* 6.1 0.2 - - + -
148A VAL* 3.5 4.4 - - - +
149A VAL* 3.0 73.0 + - + +
151A MET* 4.1 23.1 - - + -
215A THR* 4.8 5.8 - - + -
613A LEU* 3.9 33.9 - - + -
618A VAL* 4.8 14.6 - - + -
621A LEU* 4.2 13.7 - - + -
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Residues in contact with VAL 131 (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* 1.4 82.5 - - - +
132A GLN* 1.4 60.1 + - - +
146A PHE* 3.9 20.9 - - + -
147A ARG 3.3 6.5 - - - +
148A VAL* 3.6 30.1 - - + -
205A VAL* 3.7 15.0 - - + -
207A VAL* 4.6 11.0 - - + -
215A THR* 5.3 7.6 - - + +
216A GLU 5.1 2.2 - - - +
217A HIS* 3.2 57.6 + - + +
613A LEU* 5.5 0.7 - - - +
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Residues in contact with GLN 132 (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* 4.3 6.3 - - + -
131A VAL* 1.4 71.8 - - - +
133A THR* 1.3 69.6 + - - +
146A PHE* 3.2 4.7 - - - +
147A ARG* 2.7 77.7 + - + +
217A HIS* 5.1 0.9 - - - -
596A ALA* 4.5 6.5 + - - +
598A ARG* 3.8 30.4 - - - +
610A ASP* 5.7 2.0 - - - +
613A LEU* 4.1 29.2 - - + +
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Residues in contact with THR 133 (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 5.8 0.2 - - - -
132A GLN* 1.3 74.1 - - - +
134A ASP* 1.3 65.7 + - - +
135A LYS* 3.1 19.9 + - - +
136A SER* 5.3 0.5 - - - -
138A TYR* 3.7 9.0 - - - +
144A VAL* 4.6 3.4 - - + -
145A LYS 3.5 4.3 - - - +
146A PHE* 3.7 21.5 - - + -
205A VAL* 5.3 2.2 - - + -
217A HIS* 2.8 38.1 + - + +
218A PRO 4.8 0.5 + - - -
219A PHE* 4.5 16.6 - - + -
598A ARG* 3.5 19.4 + - - -
610A ASP* 4.2 10.3 + - - +
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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