Contacts of the helix formed by residues 438 - 457 (chain A) in PDB entry 6DMY
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 SER 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ASP* 4.0 8.3 + - - -
437A VAL* 1.3 67.0 - - - +
439A VAL* 1.3 64.2 + - - +
440A ILE* 3.2 7.6 - - - -
441A ARG* 3.1 43.7 + - - +
442A VAL* 3.4 14.5 + - - +
501A GLN* 6.1 1.0 - - - +
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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
----------------------------------------------------------
437A VAL* 3.0 29.3 + - + +
438A SER* 1.3 72.4 - - - +
440A ILE* 1.3 57.6 + - - +
442A VAL* 3.1 10.9 + - + +
443A ALA* 2.9 33.1 + - + +
1809A Y01 5.2 13.5 - - + -
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Residues in contact with ILE 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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438A SER* 4.9 5.4 - - - -
439A VAL* 1.3 78.7 - - - +
441A ARG* 1.3 65.9 + - + +
443A ALA* 4.6 7.4 - - + +
444A SER* 2.4 46.6 + - - +
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A SER* 3.1 31.9 + - - +
440A ILE* 1.3 83.7 - - + +
442A VAL* 1.3 60.8 + - + +
444A SER* 3.9 4.1 - - - -
445A GLY* 2.9 23.7 + - - -
501A GLN* 5.7 6.9 - - - +
505A PHE* 3.9 20.1 - - + -
1139A MET* 3.7 23.3 + - - +
1140A LEU* 4.1 8.9 + - - +
1141A ALA 3.3 25.1 + - - -
1142A GLY 4.0 5.3 + - - -
1143A SER* 3.8 24.6 - - - +
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 5.9 2.9 - - + -
438A SER 3.5 16.2 - - - +
439A VAL* 3.1 13.6 + - + +
441A ARG* 1.3 77.2 - - + +
443A ALA* 1.3 60.7 + - - +
445A GLY* 3.2 2.8 + - - -
446A TYR* 3.0 52.4 + - + +
500A THR 5.8 3.6 - - - +
504A PRO* 4.9 9.0 - - + -
505A PHE* 3.7 28.4 - - + -
1809A Y01 4.6 28.7 - - + -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 2.9 20.9 + - + +
440A ILE* 4.5 9.0 - - + +
442A VAL* 1.3 77.4 - - - +
444A SER* 1.3 58.9 + - - +
446A TYR* 3.3 9.2 + - - +
447A LEU* 2.9 37.8 + - + +
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Residues in contact with SER 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ILE* 2.4 38.7 + - - +
441A ARG* 3.9 5.8 - - - -
443A ALA* 1.3 77.0 - - - +
445A GLY* 1.3 57.5 + - - +
447A LEU* 3.4 10.1 + - - +
448A LEU* 3.0 28.4 + - - +
1139A MET* 4.6 8.1 - - - +
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Residues in contact with GLY 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 ARG 2.9 12.0 + - - -
442A VAL 3.2 4.4 + - - -
444A SER* 1.3 77.7 - - - +
446A TYR* 1.3 60.6 + - - +
448A LEU* 3.6 7.3 + - - +
449A MET* 3.0 24.6 + - - +
505A PHE* 4.6 4.3 - - - -
1139A MET* 3.6 34.2 - - - +
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Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A VAL* 3.0 35.5 + - + +
443A ALA* 3.3 8.3 + - - +
445A GLY* 1.3 81.7 - - - +
447A LEU* 1.3 60.3 + - - +
449A MET* 3.0 5.6 + - + +
450A LEU* 2.8 39.1 + - + +
474A VAL* 5.9 3.6 - - + -
478A ALA* 4.6 10.7 - - + -
481A VAL* 5.1 4.7 - - - +
504A PRO* 3.6 32.2 + - + +
505A PHE* 5.1 12.3 - + - -
508A LEU* 3.6 36.6 - - + +
1809A Y01 3.6 32.0 - - + +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA* 2.9 25.8 + - + +
444A SER* 3.9 7.9 - - - +
446A TYR* 1.3 72.9 - - + +
448A LEU* 1.3 61.1 + - - +
450A LEU* 3.5 14.4 + - + +
451A ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 448 (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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444A SER 3.0 17.8 + - - +
445A GLY* 3.6 8.1 - - - +
447A LEU* 1.3 78.2 - - - +
449A MET* 1.3 59.9 + - + +
451A ALA* 3.1 10.4 + - + +
452A TYR* 2.9 25.5 + - - +
1135A LEU* 3.8 42.4 - - + +
1138A LEU* 6.0 3.8 - - + -
1139A MET* 3.8 27.1 - - + -
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Residues in contact with MET 449 (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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445A GLY 3.0 16.5 + - - +
446A TYR* 3.0 17.0 + - + +
448A LEU* 1.3 79.6 - - - +
450A LEU* 1.3 57.3 + - - +
452A TYR* 3.3 15.0 + - + +
453A ALA* 2.9 28.7 + - + +
474A VAL* 4.3 15.7 - - + -
508A LEU* 3.7 32.3 - - + -
509A GLY* 5.4 0.7 - - - -
512A VAL* 4.1 24.2 - - + -
516A PHE* 5.1 2.5 - - + -
1132A SER* 4.3 29.6 - - - +
1135A LEU* 4.8 13.2 - - + -
1136A GLY* 5.0 9.2 - - - -
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Residues in contact with LEU 450 (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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446A TYR* 2.8 29.9 + - + +
447A LEU* 3.8 15.3 - - + +
449A MET* 1.3 74.3 - - - +
451A ALA* 1.3 59.7 + - - +
453A ALA* 4.5 3.1 - - + +
454A CYS* 2.9 31.7 + - - +
471A LEU* 3.4 53.2 - - + +
474A VAL* 3.7 26.0 - - + -
475A LEU* 3.9 17.5 - - + -
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Residues in contact with ALA 451 (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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447A LEU 3.0 16.0 + - - +
448A LEU* 3.1 14.6 + - + +
450A LEU* 1.3 78.8 - - - +
452A TYR* 1.3 59.1 - - - +
454A CYS* 4.0 3.3 + - - -
455A LEU* 3.5 27.4 + - + +
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Residues in contact with TYR 452 (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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448A LEU 2.9 9.5 + - - +
449A MET* 3.8 15.5 - - + +
450A LEU 3.2 0.2 - - - -
451A ALA* 1.3 76.2 - - - +
453A ALA* 1.3 61.6 + - - +
455A LEU* 2.9 26.4 + - + +
456A THR* 2.9 35.7 + - + +
516A PHE* 4.3 15.7 - + - -
1127A LEU* 5.0 2.9 + - - +
1128A ASP* 3.5 16.5 + - - -
1131A VAL* 3.4 46.1 - - + +
1132A SER* 4.6 0.9 - - - -
1135A LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 453 (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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449A MET* 2.9 18.2 + - + +
450A LEU* 4.4 3.1 - - - +
452A TYR* 1.3 73.7 - - + +
454A CYS* 1.3 63.0 + - - +
456A THR* 2.7 27.5 + - - -
457A MET* 3.8 10.9 - - - +
467A GLY 4.9 0.2 - - - +
470A GLY* 4.4 14.3 - - - +
471A LEU* 5.2 0.9 - - - +
474A VAL* 3.7 25.4 - - + -
516A PHE* 3.9 18.8 - - + -
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Residues in contact with CYS 454 (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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450A LEU 2.9 19.7 + - - +
451A ALA* 4.1 6.5 - - - +
452A TYR 3.2 0.2 - - - -
453A ALA* 1.3 77.9 - - - +
455A LEU* 1.3 69.2 + - + +
457A MET 3.5 21.5 - - - +
458A LEU* 4.0 17.2 + - - +
467A GLY* 4.8 8.1 - - - -
471A LEU* 3.7 28.0 - - + +
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Residues in contact with LEU 455 (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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451A ALA* 3.5 16.6 - - - +
452A TYR* 2.9 14.3 + - + +
454A CYS* 1.3 89.3 - - + +
456A THR* 1.3 64.8 + - - +
457A MET* 3.2 2.2 + - - -
458A LEU* 4.5 24.1 + - + +
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Residues in contact with THR 456 (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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452A TYR* 2.9 48.2 + - + +
453A ALA* 2.7 23.3 + - - -
455A LEU* 1.3 78.5 - - - +
457A MET* 1.3 75.5 + - - +
458A LEU 4.0 0.4 + - - -
459A ARG* 4.7 9.7 + - - -
516A PHE* 3.6 21.4 - - + -
1128A ASP* 4.5 10.3 - - - +
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Residues in contact with MET 457 (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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453A ALA 3.8 8.1 - - - +
454A CYS 3.5 5.2 + - - +
456A THR* 1.3 99.2 - - - +
458A LEU* 1.3 56.8 + - - +
459A ARG* 3.9 8.1 - - + +
465A SER 2.9 21.9 - - - +
466A GLN* 3.3 37.0 - - + +
467A GLY* 3.3 14.5 - - - -
470A GLY* 3.6 18.6 - - - -
515A VAL* 6.2 1.1 - - + -
516A PHE* 3.6 27.1 - - + +
519A ALA* 3.8 25.6 - - + -
1128A ASP* 6.1 0.4 - - - +
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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
------------------------------------------------------------
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