Contacts of the strand formed by residues 425 - 431 (chain B) in PDB entry 3IJE
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 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B VAL* 4.1 1.8 - - - +
85B PRO* 3.2 33.9 - - + +
86B GLN 3.2 10.8 - - - -
87B ARG* 3.6 2.0 - - - +
88B ILE* 3.4 36.1 - - + -
100B PHE* 3.7 28.9 - - + -
101B SER 4.7 3.6 - - - +
102B ILE* 3.7 27.4 - - + -
415B THR* 3.4 2.9 + - - -
416B ILE* 2.8 51.0 + - + +
424B SER* 1.3 71.4 - - - +
426B ILE* 1.3 59.3 + - - +
427B VAL* 4.0 5.8 + - + +
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 2.7 23.2 + - + +
87B ARG* 3.2 37.5 - - - +
88B ILE* 2.9 25.3 + - - +
413B SER* 4.7 13.7 - - - -
414B PHE 3.6 9.6 - - - +
415B THR* 4.6 10.1 - - - -
424B SER* 3.2 27.4 - - - +
425B LEU* 1.3 72.7 - - - +
427B VAL* 1.3 66.2 + - - +
428B GLN* 3.9 3.5 + - + +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 3.3 31.2 - - + +
90B LEU* 4.2 18.2 - - + -
100B PHE* 4.4 8.7 - - + -
413B SER* 4.4 0.7 - - - -
414B PHE* 2.7 75.2 + - + +
416B ILE* 4.4 8.1 - - + -
425B LEU* 4.0 15.9 - - + +
426B ILE* 1.3 72.5 - - - +
428B GLN* 1.3 62.0 + - - +
429B VAL* 3.4 10.8 + - + -
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.2 31.4 - - - +
87B ARG* 2.9 33.5 + - - +
88B ILE 3.2 6.9 + - - +
89B ALA* 3.6 9.3 - - + +
90B LEU 2.7 32.9 + - - +
411B GLU* 3.5 22.6 + - + +
412B LYS 3.8 0.7 - - - -
413B SER* 3.6 16.4 - - - +
426B ILE* 3.9 4.4 + - + +
427B VAL* 1.3 69.2 - - - +
429B VAL* 1.3 59.1 + - - +
430B THR* 5.0 1.3 + - - +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.5 18.4 - - + +
92B LEU* 4.9 3.1 - - + -
363B PRO* 4.7 4.5 - - + -
366B LEU* 4.1 11.7 - - + -
410B LYS 4.5 0.9 - - - +
411B GLU* 3.4 4.3 + - - +
412B LYS* 2.6 45.6 + - - +
414B PHE* 3.4 38.6 - - + -
427B VAL* 3.7 7.0 - - + +
428B GLN* 1.3 73.0 - - - +
430B THR* 1.3 64.9 + - - +
431B PHE* 3.7 39.6 + - + -
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Residues in contact with THR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU 2.9 11.3 + - - +
91B ARG* 3.4 31.7 + - + +
92B LEU 3.2 23.0 + - - -
410B LYS 6.0 0.2 - - - -
411B GLU* 3.2 29.5 - - + +
428B GLN* 3.9 1.4 + - - +
429B VAL* 1.3 74.5 - - - +
431B PHE* 1.3 72.5 + - - +
432B ASP* 3.6 3.0 + - + +
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.6 10.1 - - + +
363B PRO* 4.5 21.5 - - + -
365B GLU* 5.8 0.2 - - + -
366B LEU* 4.1 9.6 - - + -
403B VAL* 3.3 37.9 - - + -
405B GLY 5.4 0.2 - - - -
407B PRO* 3.7 24.9 - - + +
408B GLN* 3.3 39.6 - - - +
409B GLU* 4.9 7.8 - - - +
410B LYS 4.4 8.0 + - - -
412B LYS* 5.1 3.8 - - + -
429B VAL* 3.7 31.2 - - + -
430B THR* 1.3 77.1 - - - +
432B ASP* 1.3 60.8 + - - +
433B CYS* 3.3 23.0 + - - -
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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