Contacts of the helix formed by residues 405 - 410 (chain B) in PDB entry 1EJI
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 THR 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B VAL* 2.8 32.1 + - - +
334B ASN* 4.1 2.0 - - - +
335B CYS* 3.7 28.8 - - - +
338B LEU* 4.6 8.5 - - + -
357B HIS* 3.1 10.9 + - - +
403B LEU 5.8 0.2 - - - -
404B GLY* 1.3 77.3 - - - -
406B PRO* 1.3 71.1 - - - +
407B ALA 3.2 2.8 + - - -
408B LEU* 3.4 3.8 + - - +
409B THR* 2.9 29.0 + - - -
418B PHE* 3.7 31.1 - - + -
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Residues in contact with PRO 406 (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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51B ILE 5.7 0.7 - - - +
52B ALA* 4.5 6.7 - - - +
54B GLU 4.3 6.1 - - - +
55B ASN* 3.5 13.7 - - - +
257B LYS 5.3 0.2 - - - -
258B THR* 3.8 19.5 - - + +
327B TYR* 2.9 29.4 + - + +
328B GLN* 5.4 0.2 - - - +
331B VAL* 3.9 15.9 - - + -
357B HIS* 3.7 29.8 - - + -
404B GLY* 3.6 4.5 - - - -
405B THR* 1.3 92.7 - - - +
407B ALA* 1.3 65.6 + - - +
410B SER* 3.0 14.7 + - - -
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.5 33.7 - - + +
51B ILE 5.1 4.9 + - - +
54B GLU* 3.9 17.4 + - + +
55B ASN* 4.2 16.2 - - - +
56B PHE* 3.7 20.7 - - + -
404B GLY 5.7 0.9 - - - +
405B THR 3.2 1.2 + - - -
406B PRO* 1.3 83.6 - - - +
408B LEU* 1.3 62.3 + - - +
410B SER* 3.1 14.7 + - - -
411B ARG 3.6 3.5 + - - -
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Residues in contact with LEU 408 (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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47B GLY 4.7 2.7 - - - +
48B LEU* 3.7 36.1 - - + -
49B GLU* 3.6 21.5 + - + +
50B LEU* 3.7 31.4 - - + -
405B THR* 3.4 2.9 + - - +
407B ALA* 1.3 77.1 - - - +
409B THR* 1.3 66.0 + - - +
411B ARG* 2.9 34.0 + - - +
412B GLY 3.5 4.5 + - - -
413B LEU* 3.5 31.4 - - + +
418B PHE* 3.7 22.4 - - + -
421B VAL* 4.6 6.1 - - + -
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Residues in contact with THR 409 (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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15A TRP* 3.5 13.0 - - + -
327B TYR* 3.6 23.6 - - + -
330B GLN* 3.7 20.0 - - + -
331B VAL* 3.7 21.3 - - + +
334B ASN* 2.7 35.2 + - - +
405B THR 2.9 21.8 + - - -
406B PRO 3.9 0.2 - - - -
408B LEU* 1.3 76.1 - - - +
410B SER* 1.3 58.6 + - - +
412B GLY* 2.9 18.2 + - - -
413B LEU 4.1 3.8 - - - +
418B PHE* 3.8 2.7 - - - -
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Residues in contact with SER 410 (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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15A TRP* 5.3 0.3 - - - -
18A HIS* 4.1 8.2 - - - -
22A LEU* 3.7 20.3 - - - +
55B ASN* 3.1 17.7 + - - -
56B PHE* 4.8 6.1 - - - -
260B ARG* 3.1 15.6 + - - -
327B TYR* 3.0 35.9 + - - -
406B PRO 3.0 6.3 + - - -
407B ALA 3.1 12.3 + - - -
409B THR* 1.3 79.0 - - - +
411B ARG* 1.3 57.8 + - - +
412B GLY 3.4 0.4 + - - -
477B SER* 4.7 1.9 + - - -
479B PRO* 3.9 8.6 - - - +
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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