Contacts of the helix formed by residues 374 - 379 (chain D) in PDB entry 6UZA
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 VAL 374 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D LEU* 3.8 28.5 - - + -
301D SER* 4.8 2.2 - - - +
326D LYS* 3.9 38.8 - - + +
329D VAL* 5.5 2.7 - - + -
330D VAL* 4.6 4.7 - - + -
369D ALA* 3.0 16.6 + - + +
372D TYR* 4.1 16.4 - - + +
373D GLU* 1.3 73.4 - - - +
375D LYS* 1.3 64.2 + - - +
376D LYS 4.9 0.2 - - - +
377D PHE* 3.7 25.1 - - + +
378D VAL* 3.3 25.1 + - - +
744D PHE* 4.7 0.7 - - - -
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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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326D LYS* 5.4 1.2 - - - +
373D GLU* 3.6 39.3 + - - +
374D VAL* 1.3 74.7 - - - +
376D LYS* 1.3 59.4 + - + +
378D VAL* 3.4 2.6 + - - +
379D ALA* 2.9 30.7 + - - +
740D VAL* 3.7 19.5 - - + +
741D GLU* 4.8 17.9 - - - +
744D PHE* 3.9 39.8 - - + -
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Residues in contact with LYS 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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323D MET* 4.3 19.3 - - + +
327D ASP* 5.0 10.8 - - - +
330D VAL* 3.7 31.7 - - + +
374D VAL* 3.5 1.0 - - - +
375D LYS* 1.3 75.0 - - + +
377D PHE* 1.3 62.7 + - - +
379D ALA* 3.9 4.2 - - - +
380D HIS* 3.4 23.6 + - - +
736D ASP* 6.2 2.5 - - - -
737D ASP* 5.3 10.0 - - - +
740D VAL* 3.9 32.1 - - + +
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Residues in contact with PHE 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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294D VAL* 5.2 0.2 - - + -
298D LEU* 5.9 3.4 - - + -
329D VAL* 3.6 37.0 - - + -
330D VAL* 3.5 10.3 - - + +
333D LEU* 3.7 31.7 - - + +
345D ILE* 3.9 28.3 - - + -
346D LEU* 3.7 21.8 - - + -
365D ARG* 5.0 9.2 - - + -
366D LEU* 3.8 24.0 - - + -
369D ALA* 3.7 23.6 - - + -
374D VAL* 3.7 24.8 + - + +
375D LYS 3.3 0.6 - - - -
376D LYS* 1.3 79.7 - - - +
378D VAL* 1.3 57.7 + - - +
380D HIS* 4.0 1.3 - - - +
383D CYS* 3.5 17.0 - - - +
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Residues in contact with VAL 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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366D LEU* 4.6 6.1 - - + -
369D ALA* 3.9 26.0 - - + +
370D ILE* 4.1 18.8 - - + -
374D VAL 3.3 17.9 - - - +
375D LYS 3.4 1.4 + - - +
376D LYS 3.3 0.2 - - - -
377D PHE* 1.3 81.7 - - + +
379D ALA* 1.3 55.4 + - - +
380D HIS 3.3 4.6 + - - -
383D CYS* 4.0 17.9 - - - -
384D GLN* 2.9 22.2 - - - +
387D LEU* 4.6 4.0 - - + -
743D LYS 5.2 1.1 - - - +
744D PHE* 4.0 18.8 - - + -
747D ALA* 3.7 27.7 - - + +
751D PHE* 5.5 0.2 - - + -
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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 2.9 18.0 + - - +
376D LYS* 3.8 4.2 + - - -
377D PHE 3.5 0.2 - - - -
378D VAL* 1.3 74.9 - - - +
380D HIS* 1.3 59.8 + - - +
381D PRO* 4.1 4.5 - - - +
384D GLN* 4.5 4.9 - - - +
740D VAL* 3.9 30.0 - - + +
743D LYS* 3.7 40.0 + - + +
744D PHE 4.6 1.8 - - - +
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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