Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 3JRQ
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 LEU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 4.3 19.7 - - + +
127A PRO* 1.3 77.6 - - - +
129A TYR* 1.3 60.6 + - - +
392A ASP* 3.8 33.2 - - + +
395A ALA* 4.6 0.4 - - - -
420A VAL* 3.2 11.1 - - - +
421A ASP* 3.0 62.0 + - + +
423A LYS 4.9 7.9 - - - +
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Residues in contact with TYR 129 (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 PRO* 3.8 14.8 + - + -
128A LEU* 1.3 75.6 - - - +
130A GLY* 1.3 67.4 + - - +
131A PHE* 4.7 2.7 - + - -
147A THR* 2.9 52.0 + - + -
149A PRO* 4.0 26.1 - - + +
173A PHE* 3.6 26.5 - + + -
390A GLY 3.3 24.9 + - - -
391A LYS* 3.5 37.0 + - + +
392A ASP* 2.7 32.3 + - - +
395A ALA* 3.5 7.0 - - - -
418A VAL* 4.9 0.7 - - + -
419A VAL 3.2 12.1 - - - +
420A VAL* 4.2 2.9 - - + -
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Residues in contact with GLY 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 TYR* 1.3 76.7 - - - +
131A PHE* 1.3 66.6 + - - +
395A ALA* 3.4 3.3 - - - +
396A MET* 3.5 31.2 - - - -
399A ALA* 4.1 4.5 - - - -
418A VAL* 3.4 4.3 - - - +
419A VAL 2.9 30.7 + - - +
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.7 4.7 - + - -
130A GLY* 1.3 75.9 - - - +
132A THR* 1.3 78.9 + - - +
133A SER* 4.8 5.8 - - - -
145A VAL* 3.7 27.6 - - + -
147A THR* 4.5 15.9 - - + -
391A LYS* 4.2 17.3 - - - -
396A MET* 3.4 37.7 - - + +
399A ALA* 3.8 6.7 - - - +
400A GLU* 5.6 1.7 - - - +
417A VAL 3.0 15.0 - - - +
418A VAL* 3.9 14.8 - - + -
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Residues in contact with THR 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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131A PHE* 1.3 84.7 + - - +
133A SER* 1.3 69.8 + - - +
134A ILE* 3.8 21.1 - - + -
145A VAL* 4.1 1.2 - - - +
399A ALA* 3.4 22.6 + - - +
400A GLU* 3.1 34.6 + - - +
403A SER* 3.8 10.4 + - - +
415A ILE 4.3 1.3 - - - -
416A SER* 3.4 1.7 - - - -
417A VAL* 3.0 30.5 + - - +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.6 7.3 - - - -
132A THR* 1.3 82.0 - - - +
134A ILE* 1.3 61.6 + - - +
141A MET* 4.2 10.7 - - - +
143A ASP* 3.9 17.5 + - - +
144A ALA* 4.8 0.9 - - - -
145A VAL* 4.1 14.3 - - - +
415A ILE 3.3 7.6 - - - -
416A SER* 2.9 18.0 + - - -
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Residues in contact with ILE 134 (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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132A THR* 3.8 21.1 - - + -
133A SER* 1.3 76.4 - - - +
135A CYS* 1.3 60.1 + - - +
136A GLY 4.0 4.9 - - - +
141A MET* 3.2 11.9 - - - +
400A GLU* 5.3 0.9 - - - +
403A SER* 3.9 22.0 - - - +
404A LYS* 5.8 1.1 - - + -
407A ILE* 3.7 34.3 - - + -
415A ILE* 2.9 48.1 + - + +
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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