Contacts of the strand formed by residues 410 - 415 (chain E) in PDB entry 5IJ7
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 410 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 5.1 0.4 - - - -
87E PHE* 3.8 22.2 - - + -
97E LEU* 3.8 18.4 - - + -
112E CYS* 3.7 20.4 - - + -
403E SER 4.0 0.3 - - - +
404E PHE* 3.4 6.6 - - - -
405E SER* 2.8 32.5 + - - +
408E SER 4.6 1.3 - - - -
409E SER* 1.3 87.8 - - - +
411E LEU* 1.3 62.0 + - - +
412E ILE* 4.1 7.0 - - + -
422E ARG* 3.5 50.0 - - + +
423E TRP 3.7 2.2 - - - +
424E ASP* 3.7 13.9 - - - +
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Residues in contact with LEU 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PHE* 4.1 8.5 - - + -
364E ALA* 3.9 20.6 - - + -
372E LEU* 3.8 24.2 - - + -
374E VAL* 3.7 30.3 - - + -
390E LEU* 3.9 8.7 - - + -
402E THR* 4.0 16.2 - - - -
403E SER 3.4 15.3 - - - +
404E PHE* 4.0 24.7 - - + -
410E ILE* 1.3 75.0 - - - +
412E ILE* 1.3 61.2 + - - +
421E TRP 3.6 2.1 - - - +
422E ARG* 3.7 0.5 - - - -
423E TRP* 2.8 44.8 + - + +
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Residues in contact with ILE 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL* 3.7 28.8 - - + +
87E PHE* 3.5 28.3 - - + -
99E PHE* 3.8 26.7 - - + -
118E ILE* 4.6 1.1 - - + -
402E THR* 3.1 8.0 - - - -
403E SER* 2.8 38.0 + - - +
410E ILE* 4.1 1.6 - - + -
411E LEU* 1.3 75.8 - - - +
413E ALA* 1.3 63.7 + - - +
414E VAL* 4.4 0.2 - - + -
420E ILE* 3.7 22.7 - - + -
421E TRP 3.3 1.6 - - - +
422E ARG* 3.7 39.0 - - + +
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Residues in contact with ALA 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E LEU* 4.2 22.0 - - + -
399E ILE* 3.7 28.9 - - + -
401E GLN 3.6 5.6 - - - -
402E THR* 4.3 3.4 - - + -
412E ILE* 1.3 74.0 - - - +
414E VAL* 1.3 63.4 + - - +
420E ILE* 3.5 3.8 - - - -
421E TRP* 2.9 45.8 + - + +
423E TRP* 4.9 0.2 - - - +
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Residues in contact with VAL 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LEU* 3.6 39.9 - - + +
84E GLY 4.1 10.3 - - - +
85E VAL* 3.4 45.8 - - + -
101E THR* 3.9 10.8 - - - +
399E ILE* 3.3 4.5 - - - +
400E ARG 2.9 25.5 + - - -
401E GLN 3.2 14.3 + - - +
412E ILE* 4.4 1.3 - - + -
413E ALA* 1.3 75.1 - - - +
415E CYS* 1.4 63.0 + - - +
419E SER 3.5 3.4 - - - +
420E ILE* 4.2 8.3 - - + -
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Residues in contact with CYS 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LEU* 2.9 31.6 + - - +
395E CYS* 4.4 3.8 - - - -
397E ALA* 3.9 12.6 - - + -
398E ALA 3.1 9.2 - - - +
399E ILE* 3.7 24.2 - - - -
400E ARG* 4.5 1.6 - - - +
414E VAL* 1.4 79.3 - - - +
416E ASP* 1.4 54.8 + - - +
417E ASP* 3.1 25.9 + - - +
418E ALA 3.5 7.3 + - - -
419E SER* 2.9 23.0 + - - +
421E TRP* 3.7 21.3 - - - -
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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