Contacts of the helix formed by residues 431 - 440 (chain A) in PDB entry 4TMU
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 GLY 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A PHE* 1.3 77.9 - - - +
432A MET* 1.3 65.4 - - - -
433A GLY 3.5 2.0 - - - -
434A TYR* 3.6 2.9 + - - +
435A VAL* 3.1 23.6 + - - +
490A SER 3.7 18.4 - - - -
491A ALA* 4.4 0.2 - - - +
492A LEU* 3.9 3.6 - - - -
4B T 3.8 25.0 + - - -
5B A 3.8 7.6 - - - -
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Residues in contact with MET 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLY* 1.3 68.5 - - - -
433A GLY* 1.3 68.0 + - - +
435A VAL* 3.3 1.6 + - - +
436A VAL* 3.1 37.7 + - + +
470A VAL* 4.1 23.8 - - + +
473A ILE* 3.6 45.3 - - + -
474A ARG* 4.0 27.1 - - + +
477A ILE* 4.8 4.7 - - + -
484A GLN* 4.5 16.2 - - - +
490A SER 4.6 0.2 + - - -
492A LEU* 3.7 14.1 - - + +
5B A 3.2 20.2 + - - +
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Residues in contact with GLY 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A MET* 1.3 76.5 - - - +
434A TYR* 1.3 60.7 + - - +
436A VAL* 3.4 5.9 + - - +
437A GLU* 3.1 32.3 + - - +
5B A 2.8 23.5 + - - -
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 4.7 3.8 - - + -
430A PHE* 3.6 38.4 - + + -
431A GLY* 3.6 8.6 + - - +
432A MET 3.2 0.6 - - - -
433A GLY* 1.3 73.5 - - - +
435A VAL* 1.3 67.0 + - - +
437A GLU* 2.9 32.3 + - - +
438A VAL* 3.1 25.4 + - + +
446A ARG* 3.2 60.1 + - + +
447A ILE* 3.6 16.0 - - + +
450A LEU* 4.3 2.3 - - + +
452A HIS* 2.8 37.1 + + - -
4B T 4.2 14.1 - - - +
5B A 4.4 1.0 + - - -
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA 4.6 0.4 - - - +
422A ALA* 4.3 11.4 - - + +
423A ILE* 3.7 28.3 - - + +
426A VAL* 4.3 20.4 - - + -
430A PHE* 4.0 11.9 - - + +
431A GLY 3.1 18.4 + - - +
432A MET 3.3 3.3 + - - +
434A TYR* 1.3 77.6 - - + +
436A VAL* 1.3 57.3 + - - +
438A VAL* 3.5 11.5 - - - +
439A LEU* 3.2 38.4 + - + +
473A ILE* 4.3 9.2 - - + -
492A LEU* 3.8 14.1 - - + -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A MET* 3.1 29.2 + - + +
433A GLY* 3.7 6.3 - - - +
435A VAL* 1.3 74.4 - - - +
437A GLU* 1.3 68.0 + - - +
439A LEU* 2.8 17.9 + - - +
440A ARG* 3.0 17.4 + - + +
466A GLN* 3.8 39.9 - - + +
469A TRP* 4.3 13.9 - - + -
470A VAL* 4.4 10.5 - - + +
473A ILE* 4.2 20.2 - - + -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A GLY* 3.1 21.0 + - - +
434A TYR* 2.9 26.5 + - - +
436A VAL* 1.3 78.3 - - - +
438A VAL* 1.3 63.5 + - - +
440A ARG* 3.2 10.3 + - - +
441A GLY 3.3 9.2 + - - -
442A ALA* 3.4 31.1 + - + +
444A ASN* 3.1 28.3 + - - +
447A ILE* 4.9 5.1 - - + +
17B T 5.8 3.5 - - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ALA* 4.9 6.5 - - + -
426A VAL* 4.6 15.5 - - + -
434A TYR* 3.1 28.2 + - + +
435A VAL* 3.5 12.3 - - - +
437A GLU* 1.3 76.8 - - - +
439A LEU* 1.3 60.4 + - - +
441A GLY 3.2 4.3 + - - -
447A ILE* 3.7 22.8 - - + +
452A HIS* 4.8 8.1 - - + +
455A LEU* 5.8 2.0 - - + -
457A VAL* 4.3 16.8 - - + -
458A TYR* 3.6 28.4 - - + -
459A GLY 2.9 23.9 + - - -
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LYS* 3.6 37.5 - - + +
419A ALA* 4.2 6.1 - - - -
422A ALA* 3.8 11.4 - - + -
435A VAL* 3.2 30.1 + - + +
436A VAL* 2.8 22.3 + - - +
438A VAL* 1.3 75.9 - - - +
440A ARG* 1.3 59.6 + - + +
441A GLY 3.3 0.2 - - - -
457A VAL 4.8 2.7 - - - +
459A GLY 3.3 6.8 - - - +
460A ILE* 4.4 10.5 - - + -
461A GLY* 2.7 31.3 + - - -
462A ARG 3.3 0.7 + - - -
469A TRP* 4.3 32.8 - - + +
473A ILE* 4.3 12.3 - - + -
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Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A VAL* 3.0 17.9 + - + +
437A GLU* 3.2 3.8 + - - +
439A LEU* 1.3 78.7 - - - +
441A GLY* 1.3 62.3 + - - +
442A ALA* 3.2 12.9 + - + +
461A GLY 4.0 5.6 - - - +
462A ARG* 3.1 44.8 + - - +
464A GLN 2.6 29.9 + - - -
465A SER* 3.8 4.6 - - - +
466A GLN* 3.3 38.8 - - - +
469A TRP* 4.1 7.4 - - + -
15B A 5.7 7.1 - - - -
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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