Contacts of the helix formed by residues 435 - 446 (chain A) in PDB entry 3TMH
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 PRO 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A ASP 4.3 2.5 - - - +
434A GLU* 1.3 90.9 - - + +
436A TYR* 1.3 69.0 + - - +
437A GLU* 3.5 17.0 - - + +
438A LYS* 2.7 52.4 + - + +
439A VAL* 3.1 8.9 + - - +
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Residues in contact with TYR 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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392A LEU* 3.3 10.7 + - + -
393A ASN 3.7 12.8 - - - -
394A ALA* 3.2 33.7 - - + -
400A GLY 5.4 0.4 - - - +
401A SER* 3.9 16.4 + - - +
434A GLU 3.6 2.2 + - - -
435A PRO* 1.3 71.1 - - - +
437A GLU* 1.3 70.2 + - + +
439A VAL* 3.1 2.7 + - - +
440A VAL* 2.9 50.1 + - + +
658D LYS* 3.2 50.6 + - + +
659D SER 3.4 1.2 - - - -
660D THR* 2.4 48.8 + - + -
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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
----------------------------------------------------------
435A PRO* 2.7 18.8 + - + +
436A TYR* 1.3 88.3 + - + +
438A LYS* 1.3 58.7 + - + +
440A VAL* 3.5 4.6 + - - +
441A ASP* 3.0 30.1 + - - +
658D LYS* 2.8 31.9 + - - -
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Residues in contact with LYS 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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434A GLU* 3.7 16.8 - - - +
435A PRO* 2.7 45.6 + - + +
437A GLU* 1.3 74.6 - - + +
439A VAL* 1.3 56.7 + - - +
441A ASP* 3.8 7.6 - - + +
442A ARG* 2.9 33.2 + - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 4.3 14.4 - - + -
401A SER* 3.8 23.1 - - - +
423A ILE* 5.0 3.4 - - + -
426A VAL* 4.2 10.5 - - + -
431A VAL* 3.7 43.3 - - + +
434A GLU* 3.9 11.9 - - + +
435A PRO 3.4 12.8 - - - +
436A TYR 3.4 5.4 - - - +
438A LYS* 1.3 77.0 - - - +
440A VAL* 1.3 67.2 + - - +
442A ARG* 3.1 8.7 + - - +
443A ILE* 3.0 24.7 + - + +
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Residues in contact with VAL 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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392A LEU* 3.5 26.0 - - + -
436A TYR* 2.9 45.2 + - + +
437A GLU* 3.8 5.6 - - - +
439A VAL* 1.3 74.0 - - - +
441A ASP* 1.3 65.8 + - - +
443A ILE* 3.1 8.5 + - - +
444A GLN* 3.1 43.3 + - - +
660D THR* 3.5 21.3 - - + +
662D LEU* 4.3 12.6 - - + -
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Residues in contact with ASP 441 (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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437A GLU 3.0 18.3 + - - +
438A LYS* 3.8 8.5 - - + +
440A VAL* 1.3 77.4 - - - +
442A ARG* 1.3 61.1 + - - +
444A GLN* 3.0 13.7 + - - +
445A SER* 2.5 41.5 + - - -
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Residues in contact with ARG 442 (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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426A VAL* 4.4 16.2 + - + -
427A ASN* 4.4 6.4 + - - +
429A VAL* 3.1 47.6 - - - +
431A VAL* 3.5 17.2 - - - +
434A GLU* 2.7 39.5 + - - -
438A LYS* 2.9 22.5 + - + +
439A VAL 3.1 7.4 + - - +
441A ASP* 1.3 77.0 + - - +
443A ILE* 1.3 61.5 + - - +
445A SER* 3.5 16.5 + - - -
446A SER* 3.6 8.3 + - - -
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Residues in contact with ILE 443 (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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388A TYR* 4.1 22.5 + - + -
390A PHE* 4.5 11.2 - - + -
392A LEU* 4.2 18.2 - - + -
423A ILE* 4.8 4.7 - - + -
426A VAL* 3.9 21.3 - - + -
439A VAL* 3.0 21.9 + - + +
440A VAL 3.4 7.0 - - - +
442A ARG* 1.3 75.8 - - - +
444A GLN* 1.3 64.1 + - - +
446A SER* 3.0 25.4 + - - +
450A VAL* 4.1 12.3 - - + +
452A LEU* 4.5 12.8 - - + -
662D LEU* 3.8 35.0 - - + -
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Residues in contact with GLN 444 (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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383A LYS* 4.4 11.9 + - - +
388A TYR* 5.6 2.0 - - - -
440A VAL* 3.3 32.2 - - - +
441A ASP* 3.0 10.3 + - - +
443A ILE* 1.3 73.6 - - - +
445A SER* 1.3 66.4 - - - +
446A SER 2.9 12.5 - - - +
447A GLY* 4.5 1.6 - - - -
662D LEU* 3.9 22.0 - - + +
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Residues in contact with SER 445 (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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441A ASP* 2.5 39.0 + - - -
442A ARG* 3.6 9.7 - - - -
443A ILE 3.3 0.2 - - - -
444A GLN* 1.3 77.5 - - - +
446A SER* 1.3 59.0 + - - +
447A GLY* 3.5 3.5 + - - -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 4.0 0.7 + - - -
388A TYR* 3.2 14.0 + - - -
427A ASN* 3.2 24.8 + - - -
442A ARG 3.6 2.8 + - - -
443A ILE 3.0 18.6 + - - +
444A GLN 2.9 10.4 - - - +
445A SER* 1.3 73.8 - - - +
447A GLY* 1.3 64.8 + - - +
449A ASN 3.0 14.9 + - - -
450A VAL* 3.0 23.0 - - - +
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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