Contacts of the strand formed by residues 415 - 421 (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 ILE 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR 4.3 0.7 - - - -
133A SER* 3.3 2.8 + - - -
134A ILE* 2.9 42.7 + - + +
136A GLY* 4.2 4.0 - - - -
346A SER* 4.0 1.1 - - - -
348A GLY* 3.8 13.5 - - - +
349A VAL* 4.1 18.2 - - + -
403A SER* 3.4 34.3 - - - +
406A ALA* 3.7 17.7 - - + -
407A ILE* 3.4 34.5 - - + +
411A SER* 4.1 9.9 - - - -
413A ASP 3.5 10.8 - - - +
414A ASN* 1.3 79.6 - - - +
416A SER* 1.3 60.6 + - - +
417A VAL* 4.5 2.0 - - + -
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR 3.4 7.0 - - - -
133A SER* 2.9 23.4 + - - -
141A MET* 5.0 0.2 - - - +
143A ASP* 2.7 30.9 + - - +
145A VAL* 4.1 9.2 - - - -
175A VAL* 4.1 18.2 - - - -
345A ALA* 3.1 4.6 - - - +
346A SER* 2.9 35.3 + - - +
349A VAL* 4.8 0.4 - - - +
415A ILE* 1.3 73.3 - - - +
417A VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.0 24.9 - - - +
132A THR* 3.0 13.3 + - - +
145A VAL* 5.1 1.2 - - - +
175A VAL* 5.0 0.2 - - - -
343A ILE* 4.2 5.6 - - + -
344A LEU 3.1 9.4 - - - +
345A ALA* 3.7 3.6 - - + -
349A VAL* 3.3 33.4 - - + -
399A ALA* 4.1 20.4 - - + +
402A LEU* 3.9 32.3 - - + -
403A SER* 4.9 1.6 - - - +
415A ILE* 4.5 6.5 - - + -
416A SER* 1.3 79.8 - - - +
418A VAL* 1.3 73.2 + - - +
419A VAL* 4.6 1.3 - - + +
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.9 0.7 - - + -
130A GLY 3.4 9.0 - - - +
131A PHE* 3.9 5.4 - - + -
145A VAL* 3.4 32.8 - - + -
146A SER 4.9 1.1 - - - +
147A THR* 4.3 5.8 - - + -
173A PHE* 3.9 32.8 - - + -
174A GLY 4.6 2.2 - - - +
175A VAL* 3.9 14.1 - - + +
342A LEU 3.6 0.3 - - - +
343A ILE* 3.4 5.5 - - - +
344A LEU* 2.7 44.5 + - + +
417A VAL* 1.3 74.6 - - - +
419A VAL* 1.3 66.3 + - - +
420A VAL* 4.2 11.0 - - + -
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.2 3.6 - - - +
130A GLY 2.9 29.7 + - - +
341A CYS* 4.4 7.2 - - + -
342A LEU 3.4 7.4 - - - +
343A ILE* 4.9 6.3 - - + -
362A ALA* 4.7 8.1 - - + -
366A ILE* 4.0 27.1 - - + -
395A ALA* 2.9 31.9 - - + +
398A ALA* 4.2 8.1 - - + -
399A ALA* 3.4 27.1 - - + +
402A LEU* 5.5 0.9 - - + -
417A VAL* 4.9 2.9 - - + -
418A VAL* 1.3 75.4 - - - +
420A VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 420 (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* 5.9 1.3 - - + -
128A LEU 3.2 14.1 - - - +
129A TYR* 4.2 6.1 - - + -
173A PHE* 4.4 25.1 - - + -
249A VAL* 4.8 6.3 - - + -
341A CYS* 3.1 8.4 - - - -
342A LEU* 2.9 56.7 + - + +
344A LEU* 6.0 0.9 - - + -
418A VAL* 4.2 15.5 - - + +
419A VAL* 1.3 77.6 - - - +
421A ASP* 1.3 64.7 + - - +
422A LEU* 3.2 25.4 + - + +
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Residues in contact with ASP 421 (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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128A LEU* 3.0 53.6 + - + +
335A ARG* 5.1 0.2 + - - -
340A ASP* 3.0 17.9 - - - +
341A CYS* 4.4 2.5 - - - -
366A ILE* 4.2 33.8 - - + +
392A ASP* 4.5 8.1 - - - +
395A ALA* 4.8 2.4 - - + +
419A VAL* 4.2 1.2 + - - +
420A VAL* 1.3 77.7 - - - +
422A LEU* 1.3 59.1 + - - +
423A LYS* 3.8 22.1 + - - +
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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
------------------------------------------------------------
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