Contacts of the helix formed by residues 437 - 452 (chain D) in PDB entry 6X34
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 437 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413D HIS* 3.8 38.4 - - + +
414D PHE* 5.7 2.6 - - + -
435D ALA 4.3 2.7 - - - +
436D LEU* 1.3 83.3 - - + +
438D LEU* 1.3 64.1 + - - +
439D GLU 3.2 3.5 + - - +
440D GLY* 4.5 9.9 - - - +
441D VAL* 3.2 23.2 + - + +
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Residues in contact with LEU 438 (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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436D LEU* 2.7 27.9 + - + +
437D PRO* 1.3 72.8 - - - +
439D GLU* 1.3 61.6 + - - +
441D VAL* 3.2 9.9 - - - +
442D ILE* 3.2 27.3 - - - +
510D GLU* 5.0 4.5 - - + +
511D ALA* 3.9 23.6 - - + -
514D SER* 5.2 5.8 - - - -
518D ILE* 4.4 7.4 - - + -
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Residues in contact with GLU 439 (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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437D PRO* 3.2 1.2 - - + -
438D LEU* 1.3 78.6 - - - +
440D GLY* 1.3 59.0 + - - +
442D ILE* 3.4 6.5 + - - +
443D LEU* 2.9 30.2 + - - +
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Residues in contact with GLY 440 (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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43D GLY 3.8 9.1 - - - +
44D ASN* 5.0 7.7 + - - -
410D LEU* 6.4 0.2 - - - -
437D PRO* 3.4 14.3 + - - +
439D GLU* 1.3 80.1 - - - +
441D VAL* 1.3 56.4 + - - +
443D LEU* 3.3 7.8 + - - +
444D SER* 2.9 29.1 + - - -
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Residues in contact with VAL 441 (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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410D LEU* 5.7 8.7 - - + +
411D TYR* 4.9 10.5 - - + -
414D PHE* 4.3 36.3 - - + -
437D PRO* 3.2 16.8 + - + +
438D LEU* 3.2 20.4 - - - +
440D GLY* 1.3 75.7 - - - +
442D ILE* 1.3 68.4 + - + +
444D SER* 2.5 22.6 + - - +
445D LEU* 2.9 37.4 + - + +
518D ILE* 4.8 5.8 - - + -
522D LEU* 5.6 4.0 - - + -
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Residues in contact with ILE 442 (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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438D LEU 3.2 19.7 - - - +
439D GLU* 3.4 8.0 + - - +
440D GLY 3.3 0.4 - - - -
441D VAL* 1.3 78.3 - - + +
443D LEU* 1.3 58.9 + - - +
445D LEU* 3.3 10.3 + - + +
446D GLN* 2.9 54.7 + - + +
514D SER* 4.3 18.2 - - - +
517D GLU* 4.7 12.6 - - + -
518D ILE* 3.6 34.3 - - + -
521D LEU* 5.2 5.8 - - + -
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Residues in contact with LEU 443 (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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43D GLY 3.4 20.9 - - - +
44D ASN* 4.7 0.2 - - - -
45D ARG* 4.4 20.4 - - + +
439D GLU 2.9 17.6 + - - +
440D GLY* 3.6 6.3 - - - +
441D VAL 3.3 0.2 - - - -
442D ILE* 1.3 79.6 - - - +
444D SER* 1.3 56.2 + - - +
446D GLN* 3.3 11.6 + - + +
447D ASP* 2.9 62.0 + - - +
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Residues in contact with SER 444 (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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42D PHE 5.3 0.4 - - - -
43D GLY* 3.6 23.5 - - - +
407D THR* 5.8 7.6 - - - -
410D LEU* 4.8 14.1 - - - +
411D TYR* 5.6 1.0 - - - -
440D GLY 2.9 15.0 + - - -
441D VAL* 2.5 30.0 + - - +
443D LEU* 1.3 76.0 - - - +
445D LEU* 1.3 57.9 + - - +
447D ASP* 3.3 1.7 + - - +
448D LEU* 2.9 31.8 + - - +
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Residues in contact with LEU 445 (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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407D THR* 5.7 0.2 - - - +
411D TYR* 3.2 40.2 - - + +
441D VAL* 2.9 32.8 + - + +
442D ILE* 3.8 7.4 - - + +
444D SER* 1.3 80.1 + - - +
446D GLN* 1.3 58.8 + - - +
448D LEU* 3.2 5.0 + - + +
449D ILE* 2.9 34.9 + - + +
518D ILE* 4.6 3.4 - - + +
521D LEU* 3.6 32.5 - - + +
522D LEU* 3.5 33.9 - - + +
525D ILE* 4.6 11.0 - - + -
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Residues in contact with GLN 446 (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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442D ILE* 2.9 38.6 + - - +
443D LEU* 3.8 12.7 - - + +
445D LEU* 1.3 76.1 - - - +
447D ASP* 1.3 65.3 + - - +
449D ILE* 4.0 4.1 + - - +
450D GLY* 3.8 13.7 + - - -
521D LEU* 3.8 29.4 - - + +
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Residues in contact with ASP 447 (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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41D GLY 5.0 1.7 - - - +
42D PHE* 4.9 18.4 - - + -
43D GLY 3.8 18.3 + - - +
443D LEU* 2.9 44.6 + - - +
444D SER 3.9 3.1 - - - +
446D GLN* 1.3 81.1 - - - +
448D LEU* 1.3 60.1 + - - +
450D GLY* 3.8 2.6 + - - -
451D TYR* 3.6 17.8 + - - +
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Residues in contact with LEU 448 (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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42D PHE* 5.9 0.7 - - - -
403D MET* 5.3 9.0 - - + -
407D THR* 5.9 6.3 - - - +
411D TYR* 6.0 0.4 - - - +
444D SER 2.9 18.4 + - - +
445D LEU* 3.9 2.9 - - + +
447D ASP* 1.3 77.2 - - - +
449D ILE* 1.3 64.6 + - - +
451D TYR* 3.3 13.3 + - - +
452D PHE* 3.4 29.2 - - + -
478D PHE* 6.2 2.5 - - + -
525D ILE* 4.4 17.9 - - + -
529D LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 449 (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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445D LEU 2.9 16.8 + - - +
446D GLN* 4.4 4.9 - - - +
447D ASP 3.4 0.2 - - - -
448D LEU* 1.3 77.5 - - - +
450D GLY* 1.3 61.5 + - - +
452D PHE* 3.0 27.8 + - - +
453D GLU* 4.1 1.9 + - - +
521D LEU* 3.7 30.1 - - + +
524D GLU* 3.8 13.5 - - + +
525D ILE* 3.7 42.8 - - + +
528D SER* 4.6 10.3 - - - +
529D LEU* 6.1 0.9 - - - -
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Residues in contact with GLY 450 (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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446D GLN 3.8 11.7 + - - -
447D ASP 3.8 4.0 + - - -
448D LEU 3.3 0.4 - - - -
449D ILE* 1.3 80.4 - - - +
451D TYR* 1.3 60.6 + - - +
452D PHE 4.6 0.2 - - - -
453D GLU* 3.9 15.6 - - - +
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Residues in contact with TYR 451 (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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42D PHE* 4.7 11.9 - + + -
396D GLU* 5.3 4.5 + - - +
399D GLN* 5.8 2.1 - - - +
400D ALA* 5.1 11.1 + - + +
403D MET* 3.6 36.7 - - + -
447D ASP 3.6 12.5 + - - +
448D LEU 3.3 8.9 + - - +
449D ILE 3.2 1.0 - - - -
450D GLY* 1.3 79.6 - - - +
452D PHE* 1.3 87.0 + + - +
453D GLU 3.5 4.0 + - - -
474D ARG* 3.3 60.7 + - + +
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Residues in contact with PHE 452 (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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403D MET* 4.6 8.5 - - + -
448D LEU* 3.4 25.6 - - + +
449D ILE* 3.0 15.4 + - - +
451D TYR* 1.3 100.2 - + - +
453D GLU* 1.3 58.5 + - - +
454D PRO* 4.4 2.8 - - - +
471D LEU* 4.4 21.8 - - + -
474D ARG* 3.6 35.7 - - + -
475D GLN* 4.8 3.4 - - + +
478D PHE* 3.5 42.2 - + - -
525D ILE* 6.4 0.2 - - + -
528D SER* 4.4 17.7 - - - +
529D LEU* 4.3 32.5 - - + -
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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