Contacts of the strand formed by residues 399 - 404 (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 399 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352E MET* 3.2 20.4 - - - +
353E ARG 5.3 0.7 + - - +
366E GLY* 3.7 24.4 + - - +
367E ASN 3.1 6.6 + - - +
370E GLY* 3.4 32.8 - - - +
371E LYS 3.8 11.2 - - - +
372E LEU* 4.2 12.3 - - + -
395E CYS* 4.2 7.6 - - - -
397E ALA 4.0 6.3 - - - +
398E ALA* 1.3 67.8 - - - +
400E ARG* 1.3 61.9 + - - +
401E GLN 3.8 11.0 - - - +
402E THR* 4.1 7.0 - - + -
413E ALA* 3.7 28.3 - - + -
414E VAL 3.3 7.4 - - - +
415E CYS* 3.7 18.4 - - - -
423E TRP* 6.2 0.7 - - - +
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Residues in contact with ARG 400 (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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81E PRO* 5.0 0.4 - - + -
82E LEU 3.3 26.9 - - - +
83E PHE* 3.8 35.2 - - + +
349E ILE* 3.8 14.3 - - - +
350E TRP* 2.8 29.7 + - - -
351E TYR* 3.0 28.0 + - + +
352E MET* 3.9 18.7 - - - -
353E ARG* 3.0 28.3 + - - +
398E ALA* 3.4 4.8 + - - +
399E ILE* 1.3 73.2 - - - +
401E GLN* 1.3 59.5 + - - +
414E VAL 2.9 10.0 + - - +
415E CYS 4.8 0.2 - - - -
416E ASP* 2.9 40.6 + - - +
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Residues in contact with GLN 401 (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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83E PHE 3.7 13.2 - - - +
84E GLY* 3.3 7.9 - - - -
85E VAL* 3.0 41.6 + - + +
86E GLN* 3.6 14.9 + - - +
181E GLU* 4.2 16.4 + - - -
183E LYS* 5.9 0.4 - - - +
299E ARG* 4.5 6.7 - - - +
353E ARG* 3.8 35.7 - - + +
354E PHE 5.5 1.6 + - - -
355E SER* 5.4 3.4 - - - -
399E ILE* 3.6 3.1 - - - +
400E ARG* 1.3 78.9 - - - +
402E THR* 1.3 83.7 + - - +
413E ALA* 3.6 0.3 - - - -
414E VAL* 3.2 27.5 + - + +
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Residues in contact with THR 402 (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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85E VAL* 4.0 5.6 - - - +
86E GLN* 5.3 0.7 - - - +
353E ARG 4.2 3.5 + - - +
355E SER* 2.7 38.5 + - - -
364E ALA* 3.5 17.7 + - + +
365E LEU* 4.6 0.7 - - - +
366E GLY 4.4 7.9 - - - +
372E LEU* 3.5 32.5 - - + -
399E ILE* 4.1 11.2 - - + -
401E GLN* 1.3 89.3 - - - +
403E SER* 1.3 63.8 + - - +
411E LEU* 4.0 9.2 - - + -
412E ILE 3.1 13.0 - - - +
413E ALA* 4.3 1.1 - - + -
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Residues in contact with SER 403 (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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85E VAL* 3.8 24.9 - - - -
86E GLN* 3.6 5.3 + - - -
87E PHE* 2.9 41.6 + - - +
89E TRP* 5.0 2.1 + - - -
355E SER* 3.9 4.5 - - - -
402E THR* 1.3 76.6 - - - +
404E PHE* 1.3 62.8 + - - +
411E LEU* 3.4 6.3 - - - +
412E ILE* 2.8 35.7 + - - -
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Residues in contact with PHE 404 (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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68E PHE* 4.0 22.2 - + - -
87E PHE* 3.5 9.0 - - - +
89E TRP* 2.8 30.4 + - - -
355E SER* 4.1 9.8 + - - -
356E MET 3.7 8.6 + - - +
357E ASP* 3.5 30.7 - - + -
362E MET* 3.7 22.2 - - + -
363E LEU 4.3 0.4 - - - -
364E ALA* 3.6 38.6 - - + -
374E VAL* 4.1 11.7 - - + -
403E SER* 1.3 74.9 + - - +
405E SER* 1.4 60.0 + - - +
408E SER* 3.6 25.8 - - - -
410E ILE 3.4 11.4 - - - -
411E LEU* 4.0 13.5 - - + -
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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