Contacts of the helix formed by residues 369 - 380 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363D LEU* 3.8 4.0 - - - +
367D GLY 4.1 0.7 + - - +
368D THR* 1.3 86.0 + - - +
370D GLY* 1.3 63.6 + - - +
371D GLY* 2.7 27.9 + - - -
372D ARG* 2.6 47.4 + - - +
373D ALA* 3.5 13.7 + - - +
396D LEU 5.6 1.1 - - - -
397D ARG* 3.8 35.9 - - - +
398D PRO 3.3 11.7 - - - +
399D SER* 4.5 5.6 - - - +
445D LEU* 5.8 1.2 - - - +
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Residues in contact with GLY 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LEU* 4.0 12.5 - - - +
369D ASP* 1.3 73.6 - - - +
371D GLY* 1.3 59.9 + - - -
374D GLU* 3.0 28.2 + - - +
386D LYS* 3.3 9.1 - - - +
398D PRO 2.6 20.0 + - - -
399D SER* 4.0 2.8 - - - +
400D GLY 3.7 21.3 - - - +
401D LEU* 3.7 2.8 - - - +
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Residues in contact with GLY 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D ASP* 2.7 15.5 + - - -
370D GLY* 1.3 73.7 - - - +
372D ARG* 1.3 60.4 + - - +
374D GLU* 3.8 3.1 - - - +
375D LYS* 3.5 15.9 + - - +
386D LYS* 3.4 31.8 + - - +
396D LEU 6.0 1.3 - - - -
398D PRO* 4.0 5.6 + - - +
445D LEU* 5.8 11.7 - - - -
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D GLY 5.9 0.2 - - - -
368D THR* 4.1 2.7 - - - +
369D ASP* 2.6 48.8 + - - +
371D GLY* 1.3 68.3 - - - -
373D ALA* 1.3 69.4 + - - +
375D LYS* 2.8 19.2 + - - +
376D VAL* 3.2 12.1 + - - +
397D ARG* 5.1 5.1 - - - +
432D THR* 4.0 7.2 - - + -
436D GLN* 4.0 23.8 + - - +
439D MSE 6.3 0.2 - - - -
441D THR 5.5 0.8 + - - -
443D ALA* 3.0 29.3 + - - +
444D THR* 3.5 15.8 + - - +
445D LEU* 3.6 22.3 - - + +
448D PHE* 3.6 49.7 - - + +
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LEU* 3.5 32.5 - - + -
368D THR* 4.4 5.2 - - - +
369D ASP 3.5 6.1 + - - +
370D GLY 4.1 0.9 - - - +
372D ARG* 1.3 79.6 - - - +
374D GLU* 1.3 63.0 + - - +
376D VAL* 3.4 2.0 + - - +
377D LEU* 3.2 33.2 + - + +
401D LEU* 4.1 8.7 - - + -
429D ILE* 4.9 8.5 - - + -
432D THR* 3.8 18.1 - - + +
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Residues in contact with GLU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR 5.2 6.7 - - - +
83C TYR* 5.3 11.9 - - - +
84C GLY* 5.8 2.7 - - - +
370D GLY 3.0 20.8 + - - +
371D GLY 3.8 3.3 - - - +
373D ALA* 1.3 77.2 - - - +
375D LYS* 1.3 64.4 + - - +
377D LEU* 3.5 6.6 + - - +
378D GLU* 3.1 23.4 + - + +
382D ILE 5.0 0.9 - - - +
384D CYS* 4.3 14.0 - - + +
385D ASN* 3.4 7.9 - - - -
386D LYS* 2.7 59.7 + - + +
401D LEU* 4.1 10.5 - - + +
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Residues in contact with LYS 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D GLY 3.5 8.3 + - - +
372D ARG* 2.8 11.2 + - - +
374D GLU* 1.3 78.6 - - - +
376D VAL* 1.3 66.6 + - + +
378D GLU* 3.1 34.9 + - - +
379D ALA* 3.2 26.7 + - - +
448D PHE* 5.5 3.8 - - + -
449D LYS* 4.8 35.9 - - + +
452D LEU* 5.3 9.4 - - + +
453D ALA* 5.6 7.7 - - - +
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Residues in contact with VAL 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D ARG 3.2 10.4 + - - +
373D ALA 3.7 2.9 - - - +
374D GLU 3.3 0.2 - - - -
375D LYS* 1.3 76.1 - - - +
377D LEU* 1.3 60.8 + - + +
379D ALA* 2.9 29.4 + - + +
380D CYS* 3.3 10.5 + - - -
428D GLY* 3.7 18.6 - - - +
431D LEU* 4.3 23.3 - - + -
432D THR* 3.1 31.0 - - - +
435D ILE* 4.9 0.2 - - + -
448D PHE* 3.9 24.0 - - + -
452D LEU* 4.4 17.5 - - + -
462D VAL* 6.1 0.7 - - + -
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D MSE 5.8 0.2 - - + -
373D ALA* 3.2 24.3 + - + +
374D GLU 3.8 3.1 - - - +
376D VAL* 1.3 77.0 - - + +
378D GLU* 1.3 58.9 + - - +
380D CYS* 3.2 11.1 + - + +
382D ILE* 2.8 64.9 + - + +
384D CYS* 3.8 24.0 - - - -
401D LEU* 4.3 14.8 - - + -
425D ILE* 4.1 24.2 - - + +
428D GLY* 3.9 28.5 - - - -
429D ILE* 4.8 4.5 - - + -
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Residues in contact with GLU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLY* 3.2 13.4 - - - -
85C GLY* 3.0 30.2 + - - +
86C THR* 5.7 0.2 + - - -
374D GLU* 3.1 15.3 + - + +
375D LYS* 3.1 42.7 - - - +
376D VAL 3.0 0.8 + - - -
377D LEU* 1.3 72.2 - - - +
379D ALA* 1.3 60.1 + - - +
380D CYS 2.8 10.9 + - - -
381D SER* 2.9 16.3 + - - -
382D ILE 3.6 10.1 + - - +
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Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D LYS* 3.2 16.8 + - - +
376D VAL* 2.9 15.1 + - + +
378D GLU* 1.3 78.2 - - - +
380D CYS* 1.3 56.3 + - - +
381D SER 3.5 0.6 + - - -
452D LEU* 5.3 9.9 - - + -
453D ALA* 5.6 5.6 - - + -
459D GLN* 6.2 1.8 - - - +
462D VAL* 3.3 26.5 - - + +
466D ARG* 3.4 19.4 + - - +
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Residues in contact with CYS 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D VAL* 3.3 14.1 + - - +
377D LEU* 3.2 10.7 + - + +
378D GLU 2.8 1.6 + - - -
379D ALA* 1.3 78.9 - - - +
381D SER* 1.3 68.8 + - - +
382D ILE* 3.3 16.6 + - + +
428D GLY* 5.7 0.9 - - - -
431D LEU* 4.8 7.0 - - - -
462D VAL* 3.3 30.7 - - - -
465D LEU* 3.9 32.3 - - + -
466D ARG* 3.9 14.9 - - - -
469D VAL* 3.6 14.0 - - - +
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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