Contacts of the helix formed by residues 437 - 457 (chain E) in PDB entry 6S7T
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 GLN 437 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E GLU* 4.5 11.1 - - - +
401E LEU 4.6 2.8 + - - +
402E ASP* 4.4 7.6 - - - +
403E THR* 2.9 35.9 + - - +
404E PHE* 4.4 12.7 - - + -
433E VAL 4.1 0.8 + - - -
434E LEU* 2.9 25.3 + - + +
435E MET 2.9 0.8 + - - -
436E LEU* 1.3 79.4 - - - +
438E GLU* 1.3 72.2 + - - +
439E PRO 3.6 0.2 - - - -
440E LEU* 3.8 10.8 + - + +
441E LEU* 3.4 43.1 + - + +
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Residues in contact with GLU 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.9 8.3 - - + +
79C VAL* 3.5 24.8 - - + +
239E TRP* 2.8 30.4 + - - -
376E GLU* 2.8 32.0 - - - +
401E LEU* 3.1 42.6 - - + +
402E ASP* 4.6 1.3 - - - +
406E ARG* 4.9 1.0 + - - -
435E MET* 3.0 17.0 + - - +
437E GLN* 1.3 88.8 - - + +
439E PRO* 1.3 68.2 - - + +
440E LEU 3.2 0.7 + - - -
441E LEU* 3.9 6.1 + - - +
442E VAL* 4.4 4.5 + - - +
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Residues in contact with PRO 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY 4.7 2.3 - - - -
66C PHE* 3.7 37.0 - - + -
69C LEU* 3.5 28.7 - - + -
239E TRP* 4.8 9.6 - - + -
435E MET 3.4 2.0 - - - +
436E LEU* 3.4 28.7 - - + +
438E GLU* 1.3 96.5 - - + +
440E LEU* 1.3 61.1 + - - -
442E VAL* 4.1 5.9 + - + +
443E VAL* 3.3 24.4 + - - +
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Residues in contact with LEU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 5.4 4.7 - - + -
66C PHE* 5.0 12.6 - - + -
436E LEU* 3.2 36.8 - - + +
437E GLN* 4.1 9.2 - - - +
438E GLU 3.2 1.8 - - - -
439E PRO* 1.3 80.5 - - - +
441E LEU* 1.3 70.3 + - + +
443E VAL* 2.9 14.8 + - + +
444E ALA* 2.8 23.8 + - - +
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Residues in contact with LEU 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E LEU* 4.1 37.0 - - + +
402E ASP 4.6 0.7 - - - +
403E THR* 4.0 23.1 - - + -
437E GLN* 3.4 34.5 + - + +
438E GLU 4.4 6.5 - - - +
439E PRO 3.6 0.4 - - - -
440E LEU* 1.3 78.7 - - + +
442E VAL* 1.3 53.9 + - + +
444E ALA* 3.0 10.0 + - - +
445E ALA* 2.7 35.3 + - - +
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Residues in contact with VAL 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY* 3.5 32.1 - - - +
68C VAL* 3.8 18.6 - - + -
69C LEU* 5.3 7.4 - - + +
72C LEU* 5.8 3.8 - - + -
401E LEU* 4.6 16.4 - - + -
438E GLU 4.4 11.6 + - - +
439E PRO 4.1 4.9 + - - +
440E LEU 3.3 0.4 - - - -
441E LEU* 1.3 74.4 - - + +
443E VAL* 1.3 63.0 + - - +
445E ALA* 3.0 9.8 + - + +
446E PHE* 2.9 40.3 + - + -
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Residues in contact with VAL 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU 5.4 0.7 - - - +
61C SER* 2.6 37.0 + - - +
62C LEU* 3.7 50.3 - - + +
65C GLY* 3.7 9.9 - - - -
66C PHE* 4.1 11.2 - - + -
439E PRO 3.3 16.7 + - - +
440E LEU* 2.9 14.6 + - + +
442E VAL* 1.3 75.1 - - - +
444E ALA* 1.3 66.1 + - - +
446E PHE* 3.0 3.2 + - - -
447E TYR* 2.8 8.0 + - + +
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Residues in contact with ALA 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440E LEU 2.8 16.8 + - - +
441E LEU* 3.4 11.2 - - - +
443E VAL* 1.3 71.4 - - - +
445E ALA* 1.3 64.5 - - - +
447E TYR* 3.0 10.9 + - - +
448E ILE* 2.9 28.4 + - + +
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Residues in contact with ALA 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E LEU 2.7 16.8 + - - +
442E VAL* 3.3 13.5 - - + +
444E ALA* 1.3 71.0 - - - +
446E PHE* 1.3 66.0 + - + +
448E ILE* 3.0 11.6 + - - +
449E LEU* 2.9 21.7 + - - +
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Residues in contact with PHE 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C SER* 3.2 22.2 - - - +
64C MET* 3.5 33.2 - - + -
65C GLY* 4.2 6.5 - - - -
68C VAL* 3.6 20.9 - - + -
442E VAL* 2.9 49.0 + - + -
443E VAL 3.5 1.1 - - - +
445E ALA* 1.3 73.5 - - + +
447E TYR* 1.3 63.5 + - - +
449E LEU* 3.0 22.9 + - + +
450E PHE* 2.9 38.3 + + + -
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Residues in contact with TYR 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.8 29.5 + - + +
57C SER* 3.3 26.7 - - - -
58C LEU* 3.9 36.7 - - + +
61C SER* 2.9 13.8 + - - +
443E VAL* 2.8 10.7 + - + +
444E ALA* 3.3 12.6 - - - +
446E PHE* 1.3 75.9 - - - +
448E ILE* 1.3 58.9 - - + +
450E PHE* 3.0 6.1 + - - +
451E PHE* 2.7 54.8 + + + +
454E ILE* 6.2 0.4 - - + -
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Residues in contact with ILE 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E ALA* 2.9 19.6 + - + +
445E ALA* 3.0 10.1 + - - +
447E TYR* 1.3 82.4 - - + +
449E LEU* 1.3 66.2 + - + +
451E PHE* 3.0 25.5 + - + +
452E THR* 3.0 20.2 + - - +
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Residues in contact with LEU 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445E ALA 2.9 12.0 + - - +
446E PHE* 3.0 29.4 + - + +
448E ILE* 1.3 78.9 - - + +
450E PHE* 1.3 62.4 + - + +
452E THR* 3.9 15.0 - - - +
453E VAL* 3.9 10.7 - - - +
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Residues in contact with PHE 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 2.9 35.0 - - + -
36C PHE* 3.8 41.6 - + + -
57C SER* 3.3 32.8 - - - +
60C ALA* 4.4 6.7 - - + -
61C SER* 4.4 17.9 - - - -
64C MET* 5.9 1.1 - - + -
446E PHE* 2.9 41.2 + + - -
447E TYR 3.5 2.5 - - - +
449E LEU* 1.3 80.4 - - + +
451E PHE* 1.3 64.9 + - - +
452E THR 3.2 0.2 - - - -
453E VAL* 2.9 20.8 + - + +
454E ILE* 3.1 14.0 + - - +
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Residues in contact with PHE 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 4.6 22.9 - - + -
57C SER* 4.8 1.1 + - - -
447E TYR* 2.7 38.5 + + + +
448E ILE* 3.0 18.4 + - + +
450E PHE* 1.3 73.0 - - - +
452E THR* 1.3 65.0 - - - +
454E ILE* 3.0 17.5 + - + +
455E ILE* 2.9 42.5 + - + +
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Residues in contact with THR 452 (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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448E ILE* 3.0 21.1 + - - +
449E LEU* 3.9 10.4 - - - +
451E PHE* 1.3 77.3 - - - +
453E VAL* 1.3 59.7 + - + +
455E ILE* 3.0 17.9 + - + +
456E TYR* 2.8 31.4 + - + +
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Residues in contact with VAL 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 4.2 24.5 - - + -
40C GLU* 4.8 11.9 - - + -
449E LEU 3.9 13.9 - - - +
450E PHE* 2.9 12.7 + - + +
452E THR* 1.3 77.4 - - + +
454E ILE* 1.3 59.0 + - - +
456E TYR* 2.9 25.7 + - + +
457E VAL* 3.4 23.1 + - + +
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Residues in contact with ILE 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 3.9 16.4 - - + -
40C GLU* 5.1 2.7 - - - +
50C ILE* 5.0 6.5 - - + -
53C GLU* 4.0 42.6 - - + +
54C LEU* 3.7 31.2 - - + -
57C SER* 4.2 15.5 - - - +
447E TYR* 6.1 0.2 - - + -
450E PHE 3.1 11.1 + - - +
451E PHE* 3.0 22.4 + - + +
453E VAL* 1.3 75.8 - - - +
455E ILE* 1.3 60.2 + - + +
456E TYR 3.6 0.2 + - - -
457E VAL* 4.1 4.5 - - - +
458E ARG* 3.2 31.8 + - - +
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Residues in contact with ILE 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E PHE* 2.9 34.2 + - + +
452E THR* 3.0 23.3 + - + +
454E ILE* 1.3 78.7 - - + +
456E TYR* 1.3 61.4 + - + +
457E VAL 3.6 0.4 - - - -
458E ARG* 4.0 14.2 + - + +
459E LEU* 3.4 29.8 - - + +
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Residues in contact with TYR 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E THR* 2.8 18.6 + - + +
453E VAL* 2.9 15.5 + - + +
455E ILE* 1.3 79.3 - - + +
457E VAL* 1.3 70.9 + - + +
458E ARG 3.1 7.1 + - - -
459E LEU* 3.7 25.4 + - + +
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Residues in contact with VAL 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU* 3.6 29.2 - - + +
45C LYS* 4.8 8.3 - - - +
48C ARG* 3.9 27.8 + - - +
453E VAL* 3.7 20.2 - - + +
454E ILE* 4.1 3.8 - - - +
456E TYR* 1.3 89.8 - - + +
458E ARG* 1.3 83.3 + - - +
459E LEU 3.4 3.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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