Contacts of the helix formed by residues 434 - 443 (chain F) in PDB entry 2JG7
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 434 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279F ASP* 3.1 14.4 + - - +
432F THR* 3.3 11.2 + - - +
433F LYS* 1.3 75.3 - - - +
435F LEU* 1.3 65.2 + - - +
436F GLY* 3.0 8.5 + - - -
437F ARG* 2.7 57.0 + - + +
438F VAL* 3.1 16.1 + - - +
440F ARG* 4.2 5.0 + - - -
435H LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433F LYS 3.4 6.2 + - - -
434F ASP* 1.3 73.0 + - - +
436F GLY* 1.3 62.5 + - - +
438F VAL* 3.3 13.5 + - - +
439F PHE* 3.4 41.9 - - + -
495G ILE* 4.7 5.4 - - + -
496G ASN 4.1 10.5 - - - +
497G TYR* 4.1 10.3 - - + -
432H THR 4.4 7.9 - - - +
433H LYS* 4.2 20.8 + - + +
435H LEU* 4.2 20.0 - - + +
438H VAL* 4.2 27.6 - - + -
439H PHE* 5.6 0.2 - - + -
455H ASN* 3.8 26.0 - - - +
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Residues in contact with GLY 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F ASP* 3.0 7.3 + - - -
435F LEU* 1.3 74.8 - - - +
437F ARG* 1.3 64.9 + - - +
439F PHE 3.4 1.4 + - - -
440F ARG* 3.0 40.7 + - - +
497G TYR* 3.3 32.1 + - - -
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Residues in contact with ARG 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F PHE* 3.5 49.6 - - - +
278F GLU* 5.2 0.6 - - - +
279F ASP* 3.5 12.3 + - - -
412F GLU* 2.8 30.6 + - - +
416F PHE* 4.3 3.7 - - + -
430F ILE* 4.1 10.3 - - + -
432F THR* 3.0 26.8 + - + -
434F ASP* 2.7 39.6 + - + +
436F GLY* 1.3 71.5 - - - +
438F VAL* 1.3 63.9 + - - +
440F ARG* 3.3 15.7 + - - +
441F TRP* 2.9 25.9 + - - +
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Residues in contact with VAL 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E ILE* 4.3 25.6 - - + -
430F ILE* 4.4 3.4 - - - -
432F THR* 4.0 11.7 - - + +
434F ASP 3.1 15.3 + - - +
435F LEU* 3.5 8.1 - - - +
436F GLY 3.3 0.2 - - - -
437F ARG* 1.3 77.8 - - - +
439F PHE* 1.3 70.0 + - + +
441F TRP* 3.3 8.4 - - - +
442F LEU* 3.1 27.8 + - + +
454F VAL* 3.8 34.8 - - + -
435H LEU* 4.2 22.2 - - + -
439H PHE* 5.9 0.2 - - + -
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Residues in contact with PHE 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ILE* 5.5 7.0 - - + -
495E ILE* 5.2 1.8 - - + -
435F LEU* 3.4 35.2 - - + -
436F GLY 3.4 1.8 + - - +
437F ARG 3.3 0.4 - - - -
438F VAL* 1.3 86.8 - - + +
440F ARG* 1.3 61.4 + - - +
442F LEU* 3.4 21.3 + - + +
443F GLY* 2.9 25.5 + - - -
148G ALA* 3.6 28.0 - - + -
150G ILE* 6.2 2.0 - - + -
495G ILE* 4.0 26.9 - - + -
497G TYR* 3.6 42.7 + + + -
439H PHE* 4.3 20.2 - + - -
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Residues in contact with ARG 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F GLU* 2.7 45.9 + - - +
416F PHE* 4.3 4.0 - - + -
434F ASP* 4.2 5.1 + - - -
436F GLY* 3.0 39.2 + - - +
437F ARG* 3.3 22.5 + - - +
439F PHE* 1.3 75.8 - - - +
441F TRP* 1.3 62.1 + - - +
443F GLY* 3.2 12.3 + - - -
445F LYS* 4.0 3.7 + - + +
446F GLY* 3.3 18.0 + - - -
497G TYR* 4.6 14.5 + - + -
498G SER* 6.2 1.2 - - - +
499G LYS* 5.6 5.9 - - - +
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Residues in contact with TRP 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ILE* 4.0 8.1 - - + -
416F PHE* 3.5 39.6 - + + -
419F ASN* 3.6 22.9 - - + -
428F SER* 3.4 26.7 - - - -
429F SER 3.8 8.3 - - - -
430F ILE* 3.5 40.7 - - + +
437F ARG 2.9 11.6 + - - +
438F VAL 3.3 7.6 - - - +
440F ARG* 1.3 76.9 - - - +
442F LEU* 1.3 60.9 + - + +
443F GLY 4.1 0.2 - - - +
446F GLY* 3.4 3.8 - - - -
447F SER* 3.1 52.5 + - - +
452F VAL* 3.3 27.7 - - + +
453F ASN 3.0 18.4 + - - -
454F VAL* 3.6 16.6 - - + -
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Residues in contact with LEU 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ILE* 4.1 17.7 - - + -
152E GLN* 3.4 20.6 + - + +
154E ASN* 3.2 18.7 + - - -
489E ARG* 5.7 0.3 + - - -
491E SER* 4.7 2.6 + - - -
493E CYS* 3.9 17.3 - - + -
495E ILE* 3.6 30.1 - - + -
438F VAL* 3.1 22.7 + - + +
439F PHE* 3.7 19.1 - - + +
440F ARG 3.2 0.2 - - - -
441F TRP* 1.3 81.5 - - + +
443F GLY* 1.3 61.2 + - - +
447F SER 5.7 0.4 - - - +
452F VAL* 3.7 34.3 - - + +
454F VAL* 4.3 7.0 - - + -
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Residues in contact with GLY 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLN* 4.4 5.6 - - - -
154E ASN* 3.5 9.4 + - - -
489E ARG* 4.0 5.4 + - - -
439F PHE 2.9 17.1 + - - -
440F ARG* 3.2 5.1 + - - -
441F TRP 4.1 0.5 - - - +
442F LEU* 1.3 82.9 - - - +
444F PRO* 1.3 71.4 - - - +
445F LYS 3.3 2.7 - - - -
446F GLY* 3.1 19.2 + - - -
447F SER 4.6 0.9 - - - +
497G TYR* 6.1 0.2 - - - -
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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