Contacts of the strand formed by residues 411 - 417 (chain B) in PDB entry 5NET
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 ARG 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLY 3.3 16.3 + - - +
362B ASP 2.4 43.9 + - - -
363B THR* 3.2 41.5 + - - +
364B GLU* 4.5 5.5 - - - +
366B LEU* 6.3 0.2 - - + -
407B GLU* 4.9 5.1 + - - +
408B ARG* 5.3 8.3 - - - +
409B ARG 3.9 0.4 + - - +
410B SER* 1.3 76.9 + - - +
412B HIS* 1.3 66.7 + - - +
413B ILE* 3.5 14.8 + - + +
426B LEU 3.3 4.9 - - - +
427B LEU* 4.0 0.7 - - - -
428B VAL* 2.9 35.8 + - + +
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Residues in contact with HIS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 4.1 0.9 - - - +
361B GLY* 3.0 22.2 - - - +
410B SER* 4.3 21.8 + - - -
411B ARG* 1.3 77.8 - - - +
413B ILE* 1.3 61.7 + - - +
414B ILE* 5.3 3.9 - - + +
426B LEU 3.7 3.8 - - - -
427B LEU* 3.5 27.2 - - + +
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Residues in contact with ILE 413 (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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359B VAL* 3.6 26.2 - - + -
360B LEU 3.5 11.2 - - - +
362B ASP* 3.7 16.8 - - + -
366B LEU* 3.7 29.8 - - + -
401B VAL* 5.2 1.8 - - + -
411B ARG* 3.8 17.0 - - + +
412B HIS* 1.3 76.0 - - - +
414B ILE* 1.3 73.6 + - - +
415B ILE* 5.0 0.2 - - + -
425B GLU* 4.5 0.2 - - - +
426B LEU* 2.7 56.1 + - + +
428B VAL* 3.7 23.6 - - + -
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Residues in contact with ILE 414 (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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358B GLU 3.4 4.7 - - - +
359B VAL* 3.5 0.7 - - - -
360B LEU* 2.9 48.7 + - + +
412B HIS* 5.3 3.6 - - + +
413B ILE* 1.3 84.9 - - - +
415B ILE* 1.3 64.0 + - - +
416B LYS* 4.0 17.0 + - + -
423B ALA* 3.7 27.1 - - + -
424B LEU 3.5 1.3 - - - +
425B GLU* 3.7 32.1 - - + -
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Residues in contact with ILE 415 (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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84B ILE* 3.5 2.3 - - - +
101B LEU* 4.6 3.1 - - + -
103B VAL* 4.6 11.0 - - + -
357B LEU* 3.9 32.8 - - + -
358B GLU 3.4 7.0 - - - +
359B VAL* 4.4 20.0 - - + -
399B VAL* 4.1 31.2 - - + -
401B VAL* 5.9 0.2 - - + -
413B ILE* 5.0 0.2 - - + -
414B ILE* 1.3 73.5 - - - +
416B LYS* 1.3 60.8 + - - +
424B LEU* 2.6 59.5 + - + +
426B LEU* 3.6 29.6 - - + -
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Residues in contact with LYS 416 (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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84B ILE* 4.2 0.4 - - - -
357B LEU* 3.5 7.2 - - - +
358B GLU* 3.0 60.8 + - + +
360B LEU* 3.7 22.0 - - + -
414B ILE* 4.1 13.5 - - + -
415B ILE* 1.3 76.0 - - - +
417B PRO* 1.3 75.5 + - - +
419B GLY 4.8 2.6 - - - +
420B LEU 2.6 31.1 + - - +
421B GLY* 4.5 4.5 + - - +
422B ASP 3.4 14.2 + - - +
423B ALA* 3.7 8.5 - - + -
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Residues in contact with PRO 417 (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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83B GLN* 5.2 0.7 - - + +
84B ILE* 3.7 20.6 - - + -
105B VAL* 3.9 26.7 - - + -
355B VAL* 5.0 4.0 - - + -
356B GLU 3.3 9.4 - - - +
357B LEU* 4.1 3.3 - - + -
358B GLU* 4.1 0.7 - - - -
416B LYS* 1.3 103.7 + - - +
418B VAL* 1.3 66.4 + - - +
419B GLY 3.3 0.7 + - - -
420B LEU* 3.3 35.9 + - + -
422B ASP* 3.3 20.2 - - + +
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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