Contacts of the helix formed by residues 369 - 380 (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 ASP 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B LEU* 3.8 4.6 - - - +
367B GLY 4.1 0.8 + - - -
368B THR* 1.3 86.6 + - - +
370B GLY* 1.3 61.9 + - - +
371B GLY* 2.6 29.4 + - - -
372B ARG* 2.7 43.1 + - - +
373B ALA* 3.5 13.0 + - - +
397B ARG* 3.9 16.5 + - - +
398B PRO 3.3 17.5 - - - +
399B SER* 4.3 7.9 - - - +
436B GLN* 4.4 0.6 + - - -
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Residues in contact with GLY 370 (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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363B LEU* 4.0 12.8 - - - -
369B ASP* 1.3 75.3 - - - +
371B GLY* 1.3 61.2 + - - +
374B GLU* 3.0 27.5 + - - +
386B LYS* 3.5 10.1 - - - +
398B PRO 3.5 9.1 + - - -
399B SER* 3.7 6.5 - - - +
400B GLY 3.7 24.0 - - - -
401B LEU* 4.2 2.3 - - - +
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Residues in contact with GLY 371 (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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369B ASP* 2.6 16.6 + - - +
370B GLY* 1.3 73.6 - - - +
372B ARG* 1.3 61.5 + - - +
374B GLU* 3.8 5.5 - - - +
375B LYS* 3.5 15.2 + - - +
386B LYS* 4.3 10.1 - - - +
396B LEU 4.6 13.2 - - - -
397B ARG* 4.8 9.6 - - - -
398B PRO* 4.5 5.1 - - - +
445B LEU* 4.2 13.3 - - - +
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Residues in contact with ARG 372 (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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368B THR* 4.1 3.4 - - - +
369B ASP* 2.7 38.6 + - - +
371B GLY* 1.3 68.4 - - - +
373B ALA* 1.3 68.1 + - - +
375B LYS* 2.9 17.4 + - - +
376B VAL* 3.2 12.3 + - - +
397B ARG* 2.6 36.7 - - - +
432B THR* 4.0 2.9 - - + -
436B GLN* 2.8 38.6 + - - +
439B MSE 4.6 7.3 - - - +
443B ALA* 3.3 25.7 + - - +
444B THR 4.0 8.8 + - - -
445B LEU* 3.7 14.1 - - + +
448B PHE* 3.7 34.7 - - + -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 3.5 31.6 - - + -
368B THR* 4.4 5.4 - - - +
369B ASP 3.5 6.7 + - - +
370B GLY 4.2 1.3 - - - +
372B ARG* 1.3 78.2 - - - +
374B GLU* 1.3 62.4 + - - +
376B VAL* 3.4 1.6 + - - +
377B LEU* 3.2 30.8 + - - +
401B LEU* 4.2 8.7 - - + -
429B ILE* 4.8 12.6 - - + -
432B THR* 3.8 18.5 - - + +
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Residues in contact with GLU 374 (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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82A TYR 5.0 3.0 - - - +
83A TYR* 5.3 8.1 - - - -
84A GLY* 5.7 4.0 - - - +
370B GLY 3.0 21.0 + - - +
371B GLY 3.8 5.9 - - - +
373B ALA* 1.3 76.8 - - - +
375B LYS* 1.3 65.9 + - - +
377B LEU* 3.6 3.0 + - - +
378B GLU* 3.2 22.8 + - + +
384B CYS* 4.5 9.8 - - + +
385B ASN* 3.1 16.4 - - - +
386B LYS* 2.4 62.3 + - - +
401B LEU* 4.2 13.4 - - + +
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Residues in contact with LYS 375 (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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371B GLY 3.5 8.4 + - - +
372B ARG 2.9 10.0 + - - +
374B GLU* 1.3 80.6 - - - +
376B VAL* 1.3 64.4 + - - +
378B GLU* 3.2 32.6 + - - +
379B ALA* 3.2 23.0 + - - +
445B LEU* 6.0 1.8 - - + -
448B PHE* 4.8 10.3 - - + -
449B LYS* 4.4 40.8 - - + +
452B LEU* 4.4 23.1 - - + +
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Residues in contact with VAL 376 (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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372B ARG 3.2 4.5 + - - +
373B ALA 3.8 2.7 - - - +
374B GLU 3.4 0.2 - - - -
375B LYS* 1.3 75.3 - - - +
377B LEU* 1.3 60.0 + - + +
379B ALA* 2.9 29.1 + - + +
380B CYS* 3.3 12.3 + - - -
428B GLY* 3.7 17.5 - - - +
431B LEU* 4.3 22.7 - - + -
432B THR* 3.0 32.1 - - - +
435B ILE* 4.9 2.5 - - + -
448B PHE* 3.7 29.4 - - + -
452B LEU* 4.5 16.8 - - + -
462B VAL* 6.0 0.7 - - + -
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Residues in contact with LEU 377 (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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373B ALA 3.2 19.1 + - - +
374B GLU 3.9 3.4 - - - +
376B VAL* 1.3 76.2 - - - +
378B GLU* 1.3 58.9 + - - +
380B CYS* 3.2 10.8 + - + +
382B ILE* 2.8 65.7 + - + +
384B CYS* 4.1 12.6 - - + -
401B LEU* 3.7 28.0 - - + -
425B ILE* 4.1 24.9 - - + +
428B GLY* 3.9 28.9 - - - -
429B ILE* 4.8 6.3 - - + -
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Residues in contact with GLU 378 (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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84A GLY* 2.9 15.4 - - - -
85A GLY* 2.8 32.6 + - - +
86A THR* 5.5 0.3 + - - -
374B GLU* 3.2 15.9 + - + +
375B LYS* 3.2 42.1 - - - +
376B VAL 3.0 0.6 - - - -
377B LEU* 1.3 73.3 - - - +
379B ALA* 1.3 57.6 - - - +
380B CYS 2.9 10.7 + - - -
381B SER* 2.9 15.6 + - - -
382B ILE 3.7 10.3 + - - +
383B ALA* 5.4 2.7 - - - +
384B CYS 6.0 0.9 - - - +
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Residues in contact with ALA 379 (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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375B LYS* 3.2 12.6 + - - +
376B VAL* 2.9 12.7 + - - +
378B GLU* 1.3 78.9 - - - +
380B CYS* 1.3 58.3 + - - +
381B SER 3.5 0.4 + - - -
452B LEU* 4.2 22.7 - - + -
459B GLN* 6.1 2.0 - - - +
462B VAL* 3.2 25.7 - - + +
466B ARG* 3.4 19.7 + - - +
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Residues in contact with CYS 380 (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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376B VAL* 3.5 20.9 - - - -
377B LEU* 3.2 8.9 + - + +
378B GLU 2.9 2.0 + - - -
379B ALA* 1.3 78.4 - - - +
381B SER* 1.3 70.1 + - - +
382B ILE* 3.3 10.8 + - + +
428B GLY* 5.8 1.1 - - - -
431B LEU* 4.9 1.1 - - - -
462B VAL* 3.3 31.9 - - - -
465B LEU* 4.2 27.4 - - + -
466B ARG* 3.9 17.7 - - - +
469B VAL* 3.5 18.5 - - - +
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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