Contacts of the helix formed by residues 435 - 446 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433E ASP 4.3 2.5 - - - +
434E GLU* 1.3 91.4 - - + +
436E TYR* 1.3 67.0 + - - +
437E GLU* 3.5 16.4 - - + +
438E LYS* 2.7 31.5 + - + +
439E VAL* 3.0 11.7 + - - +
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Residues in contact with TYR 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E LEU* 3.3 16.6 + - + -
393E ASN 3.7 12.6 - - - -
394E ALA* 3.1 35.9 - - + -
400E GLY 5.4 0.4 - - - +
401E SER* 3.8 16.3 + - - +
434E GLU 3.6 2.0 + - - -
435E PRO* 1.3 69.8 - - - +
437E GLU* 1.3 74.8 + - + +
439E VAL* 3.2 2.7 + - - +
440E VAL* 2.9 40.3 + - + +
658H LYS* 3.5 49.1 - - + +
659H SER 3.3 5.0 - - - -
660H THR* 2.3 50.6 + - + -
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E PRO* 3.5 17.6 - - + +
436E TYR* 1.3 89.0 + - + +
438E LYS* 1.3 63.7 + - - +
439E VAL 3.1 0.2 + - - -
440E VAL* 3.3 4.6 + - - +
441E ASP* 2.9 24.9 + - - +
658H LYS* 2.5 35.1 + - - -
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Residues in contact with LYS 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E GLU* 3.9 13.2 - - - +
435E PRO* 2.7 35.4 + - + +
437E GLU* 1.3 76.6 - - - +
439E VAL* 1.3 57.3 + - - +
441E ASP* 3.4 7.9 + - - +
442E ARG* 2.9 31.0 + - - +
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Residues in contact with VAL 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E LEU* 4.3 15.7 - - + -
401E SER* 3.8 17.9 - - - +
423E ILE* 4.9 3.4 - - + -
426E VAL* 4.3 10.8 - - + -
431E VAL* 3.7 42.4 - - + +
434E GLU* 3.8 16.8 - - + +
435E PRO 3.0 14.7 + - - +
436E TYR 3.5 4.7 - - - +
438E LYS* 1.3 74.1 - - - +
440E VAL* 1.3 68.6 + - - +
442E ARG* 2.9 20.1 + - - +
443E ILE* 2.9 16.1 + - + +
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Residues in contact with VAL 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E LEU* 3.7 18.2 - - + -
436E TYR* 2.9 48.3 + - + +
437E GLU* 3.7 4.9 - - - +
439E VAL* 1.3 73.5 - - - +
441E ASP* 1.3 67.2 + - - +
443E ILE* 2.9 18.7 + - - +
444E GLN* 3.0 36.1 + - + +
660H THR* 3.6 24.2 - - + +
662H LEU* 4.6 9.2 - - + -
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Residues in contact with ASP 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E GLU 2.9 14.0 + - - +
438E LYS* 3.4 12.6 - - - +
440E VAL* 1.3 78.3 - - - +
442E ARG* 1.3 60.9 + - - +
444E GLN* 2.9 14.0 + - - +
445E SER* 2.5 40.2 + - - -
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Residues in contact with ARG 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E VAL* 4.4 16.7 + - + +
427E ASN* 4.4 6.6 + - - +
429E VAL* 3.3 41.2 - - - +
431E VAL* 3.4 18.8 - - - +
434E GLU* 2.7 41.6 + - - -
438E LYS* 2.9 17.3 + - + +
439E VAL* 2.9 9.5 + - - +
441E ASP* 1.3 77.7 - - - +
443E ILE* 1.3 62.8 + - - +
445E SER* 3.5 17.2 + - - -
446E SER* 3.6 7.4 + - - -
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Residues in contact with ILE 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E TYR* 4.2 20.0 + - + -
390E PHE* 4.5 11.2 - - + -
392E LEU* 4.2 19.7 - - + -
423E ILE* 4.7 10.1 - - + -
426E VAL* 3.9 21.3 - - + -
439E VAL* 2.9 19.2 + - + +
440E VAL* 2.9 8.6 + - - +
442E ARG* 1.3 75.8 - - - +
444E GLN* 1.3 65.1 + - - +
446E SER* 3.0 24.5 + - - +
450E VAL* 4.2 13.7 - - + +
452E LEU* 4.6 7.4 - - + -
662H LEU* 3.8 34.3 - - + -
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Residues in contact with GLN 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E LYS* 4.4 10.9 + - - +
388E TYR* 5.6 1.8 - - - -
440E VAL* 3.3 33.1 - - - +
441E ASP* 2.9 10.8 + - - +
443E ILE* 1.3 73.6 - - - +
445E SER* 1.3 67.1 + - - +
446E SER 2.9 15.4 - - - +
447E GLY* 4.5 1.2 - - - -
662H LEU* 4.0 21.6 - - + +
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Residues in contact with SER 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E ASP* 2.5 39.6 + - - -
442E ARG* 3.5 9.9 - - - -
443E ILE 3.3 0.2 - - - -
444E GLN* 1.3 77.5 - - - +
446E SER* 1.3 58.6 + - - +
447E GLY* 3.5 3.6 + - - -
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Residues in contact with SER 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383E LYS* 4.0 1.0 + - - -
388E TYR* 3.2 9.2 + - - -
427E ASN* 3.3 23.9 + - - -
442E ARG 3.6 2.2 + - - -
443E ILE 3.0 11.3 + - - +
444E GLN 2.9 10.4 + - - +
445E SER* 1.3 76.1 - - - +
447E GLY* 1.3 67.1 + - - +
449E ASN 2.9 14.4 + - - -
450E VAL* 3.0 30.9 - - - +
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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