Contacts of the helix formed by residues 369 - 380 (chain C) 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 ASP 369 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363C LEU* 3.7 3.8 - - - +
367C GLY 4.1 1.0 + - - +
368C THR* 1.3 85.3 + - - +
370C GLY* 1.3 63.0 + - - +
371C GLY* 2.6 29.0 + - - +
372C ARG* 2.6 45.4 + - - +
373C ALA* 3.5 13.7 + - - +
397C ARG* 3.8 32.7 + - + +
398C PRO* 4.8 4.5 - - - -
399C SER* 4.2 13.9 - - - +
436C GLN* 4.8 0.2 + - - -
445C LEU* 4.5 2.0 - - - +
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Residues in contact with GLY 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C LEU* 3.9 4.0 - - - +
369C ASP* 1.3 76.0 - - - +
371C GLY* 1.3 56.2 + - - +
374C GLU* 3.0 32.9 + - - +
386C LYS* 3.5 10.5 - - - +
398C PRO* 4.0 2.0 - - - -
399C SER* 3.5 13.9 - - - +
400C GLY 3.7 22.7 - - - -
401C LEU* 3.6 11.4 - - - +
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Residues in contact with GLY 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C ASP* 2.6 15.6 + - - -
370C GLY* 1.3 73.7 - - - +
372C ARG* 1.3 60.7 + - - +
374C GLU* 3.8 5.2 - - - +
375C LYS* 3.6 15.8 + - - +
386C LYS* 4.0 23.7 + - - +
398C PRO* 4.1 7.5 - - - +
445C LEU* 3.6 21.9 - - - +
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Residues in contact with ARG 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C THR* 4.2 1.8 - - - +
369C ASP* 2.6 48.2 + - - +
371C GLY* 1.3 67.9 - - - +
373C ALA* 1.3 68.7 + - - +
375C LYS* 2.9 18.1 + - - +
376C VAL* 3.2 12.5 + - - +
397C ARG* 3.8 10.9 - - - +
432C THR* 4.0 5.2 - - + -
436C GLN* 3.4 27.7 + - - +
439C MSE 5.9 1.6 - - - -
443C ALA* 2.9 33.6 - - - +
444C THR 3.3 22.2 + - - +
445C LEU* 3.8 24.9 - - + +
448C PHE* 3.6 50.6 - - + +
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C LEU* 3.5 32.3 - - + -
368C THR* 4.5 4.5 - - - +
369C ASP 3.5 5.3 + - - +
370C GLY 4.0 1.8 - - - +
372C ARG* 1.3 79.6 - - - +
374C GLU* 1.3 63.1 + - - +
376C VAL* 3.4 1.7 + - - +
377C LEU* 3.1 32.7 + - + +
401C LEU* 4.1 9.2 - - + -
429C ILE* 4.9 8.1 - - + -
432C THR* 3.8 19.1 - - + +
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Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C GLY 3.0 19.9 + - - +
371C GLY 3.8 4.9 - - - +
373C ALA* 1.3 76.5 - - - +
375C LYS* 1.3 65.8 + - - +
377C LEU* 3.5 2.8 + - - +
378C GLU* 3.1 23.0 + - + +
382C ILE 5.0 0.2 - - - +
384C CYS* 4.6 12.3 + - + +
385C ASN* 3.0 22.3 + - - +
386C LYS* 2.5 60.2 + - - +
401C LEU* 4.2 7.3 - - + +
82D TYR 5.0 5.9 - - - +
83D TYR* 5.5 6.7 - - - -
84D GLY* 5.9 1.1 - - - -
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Residues in contact with LYS 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C GLY 3.6 8.4 + - - +
372C ARG* 2.9 11.0 + - - +
374C GLU* 1.3 82.1 - - - +
376C VAL* 1.3 62.7 + - - +
378C GLU* 3.1 35.2 + - - +
379C ALA* 3.2 25.2 + - - +
448C PHE* 5.1 0.4 - - + -
449C LYS* 3.7 38.4 - - + -
452C LEU* 3.8 18.4 - - + +
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Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C ARG 3.2 3.5 + - - +
373C ALA 3.7 3.4 - - - +
374C GLU 3.3 0.2 - - - -
375C LYS* 1.3 76.5 - - - +
377C LEU* 1.3 60.8 + - + +
379C ALA* 2.9 27.3 + - + +
380C CYS* 3.3 12.7 + - - -
428C GLY* 3.8 16.4 - - - +
431C LEU* 4.4 23.1 - - + -
432C THR* 3.2 30.1 - - - +
435C ILE* 4.9 1.1 - - + -
448C PHE* 3.6 31.6 - - + -
452C LEU* 4.3 19.1 - - + -
462C VAL* 6.1 0.7 - - + -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ALA* 3.1 21.1 + - + +
374C GLU 3.8 3.4 - - - +
376C VAL* 1.3 79.6 - - - +
378C GLU* 1.3 59.0 + - - +
380C CYS* 3.2 10.6 + - + +
382C ILE* 2.8 64.6 + - + +
384C CYS* 4.2 14.6 - - + -
401C LEU* 3.9 27.6 - - + -
425C ILE* 4.0 22.9 - - + +
428C GLY* 3.9 28.7 - - - -
429C ILE* 4.8 3.6 - - + -
432C THR* 5.8 0.2 - - - +
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLU* 3.1 14.9 + - + +
375C LYS* 3.1 43.0 - - - +
376C VAL 3.0 0.4 - - - -
377C LEU* 1.3 71.8 - - - +
379C ALA* 1.3 60.6 + - - +
380C CYS 2.8 10.2 + - - -
381C SER* 2.9 16.1 + - - -
382C ILE 3.6 10.3 + - - +
383C ALA* 5.6 2.2 - - - +
384C CYS 6.1 0.4 - - - +
84D GLY* 3.2 14.5 - - - -
85D GLY* 3.1 29.9 + - - +
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C LYS* 3.2 16.4 + - - +
376C VAL* 2.9 15.1 + - + +
378C GLU* 1.3 79.1 - - - +
380C CYS* 1.3 56.6 + - - +
381C SER 3.5 1.0 + - - -
452C LEU* 5.2 10.8 - - + -
459C GLN* 6.2 2.5 - - - +
462C VAL* 3.3 27.5 - - + +
466C ARG* 3.4 20.4 + - - +
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Residues in contact with CYS 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C VAL* 3.5 21.1 - - - +
377C LEU* 3.2 9.7 + - + +
378C GLU 2.8 1.4 + - - -
379C ALA* 1.3 79.0 - - - +
381C SER* 1.3 70.1 + - - +
382C ILE* 3.3 12.5 + - + +
428C GLY* 5.7 1.3 - - - -
431C LEU* 4.9 2.2 - - - -
462C VAL* 3.3 29.6 - - - -
465C LEU* 4.1 30.5 - - + -
466C ARG* 3.9 14.5 - - - -
469C VAL* 3.5 18.9 - - - +
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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