Contacts of the helix formed by residues 534 - 549 (chain A) in PDB entry 6FEQ
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 VAL 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A VAL* 4.3 13.2 - - + +
446A GLU* 5.7 6.3 - - + +
449A VAL* 3.7 23.8 - - + -
450A VAL* 5.3 8.7 - - + -
532A SER 4.9 1.3 - - - +
533A VAL* 1.3 73.6 - - - +
535A SER* 1.3 59.7 + - - +
536A VAL 3.3 2.2 - - - -
537A ALA* 3.2 5.7 + - - +
538A THR* 2.6 53.1 + - + +
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Residues in contact with SER 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A VAL* 4.6 2.1 - - - +
534A VAL* 1.3 77.4 - - - +
536A VAL* 1.3 62.2 - - - +
538A THR* 3.8 6.3 - - - -
539A LEU* 3.0 28.2 + - - +
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Residues in contact with VAL 536 (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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531A GLN* 4.5 13.5 - - - +
533A VAL* 3.7 27.3 - - + +
534A VAL 3.3 0.6 - - - -
535A SER* 1.3 80.4 - - - +
537A ALA* 1.3 57.8 + - - +
539A LEU* 3.5 9.7 - - + +
540A LEU* 3.0 31.0 + - + +
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Residues in contact with ALA 537 (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 VAL* 4.0 19.7 - - + -
449A VAL* 5.9 0.4 - - + -
527A ILE* 4.5 9.1 - - + +
528A ALA* 4.4 15.0 - - + -
531A GLN* 3.8 19.1 + - - +
533A VAL 4.6 5.8 + - - +
534A VAL 3.2 8.2 + - - +
536A VAL* 1.3 77.1 - - - +
538A THR* 1.3 61.0 + - - +
540A LEU* 3.0 7.5 + - - +
541A MET* 2.8 35.7 + - + +
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Residues in contact with THR 538 (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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442A VAL* 3.7 26.3 - - + +
445A VAL* 4.0 9.3 - - - +
534A VAL* 2.6 38.4 + - + +
535A SER* 4.1 6.7 - - - -
537A ALA* 1.3 73.1 - - - +
539A LEU* 1.3 63.4 + - - +
541A MET* 3.9 3.2 + - - +
542A THR* 2.8 27.6 + - - +
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Residues in contact with LEU 539 (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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535A SER 3.0 19.4 + - - +
536A VAL* 3.5 9.0 - - + +
538A THR* 1.3 77.4 - - - +
540A LEU* 1.3 59.4 + - + +
542A THR* 2.9 25.7 + - + -
543A ILE* 3.0 28.5 + - + +
1002A D6T 3.7 62.4 - - + +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ILE* 3.9 27.6 - - + -
531A GLN* 5.6 5.4 - - - +
536A VAL* 3.0 20.8 + - + +
537A ALA* 3.0 8.3 + - - +
539A LEU* 1.3 79.0 - - + +
541A MET* 1.3 63.3 + - - +
543A ILE* 3.3 18.6 + - + +
544A CYS* 3.2 34.0 + - - -
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Residues in contact with MET 541 (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 SER 5.2 3.4 - - - +
442A VAL* 4.4 17.5 - - + -
445A VAL* 4.0 20.6 - - + -
520A ALA 4.3 1.3 - - - +
523A MET* 4.1 7.2 - - + +
524A ALA* 3.8 35.7 - - + +
527A ILE* 3.7 32.5 - - + -
537A ALA* 2.8 19.2 + - - +
538A THR 4.2 4.5 - - - +
539A LEU 3.3 0.2 - - - -
540A LEU* 1.3 75.6 - - - +
542A THR* 1.3 63.0 + - - +
544A CYS* 3.5 3.1 + - + +
545A PHE* 3.3 63.3 + - + -
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Residues in contact with THR 542 (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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439A PHE* 5.0 12.5 - - + -
442A VAL* 5.0 7.7 - - - +
538A THR* 2.8 17.2 + - - +
539A LEU* 2.9 14.3 + - + -
541A MET* 1.3 76.0 - - - +
543A ILE* 1.3 66.3 + - - +
545A PHE* 4.4 3.8 - - - +
546A VAL* 3.3 27.5 + - + +
1002A D6T 4.7 28.9 - - + +
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Residues in contact with ILE 543 (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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539A LEU* 3.0 30.0 + - + +
540A LEU* 3.6 22.9 - - + +
541A MET 3.3 0.2 - - - -
542A THR* 1.3 78.0 - - - +
544A CYS* 1.3 64.7 + - - +
546A VAL* 3.3 12.0 - - - +
547A PHE* 3.1 42.8 - - + -
1002A D6T 3.5 58.6 - - + +
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Residues in contact with CYS 544 (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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523A MET* 3.7 31.6 - - + -
527A ILE* 4.6 9.6 - - - -
540A LEU* 3.2 28.5 + - - +
541A MET* 3.5 4.9 + - - +
543A ILE* 1.3 81.1 - - - +
545A PHE* 1.3 60.9 + - + +
547A PHE* 3.5 6.6 + - - +
548A MET* 3.1 31.8 + - + +
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Residues in contact with PHE 545 (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 CYS* 3.2 46.7 - - + -
439A PHE* 3.5 33.8 - + + -
442A VAL* 4.2 9.9 - - + -
520A ALA* 4.0 21.8 - - + -
523A MET* 4.1 21.1 - - + -
541A MET* 3.3 43.9 + - + +
542A THR 3.7 0.4 + - - +
543A ILE 3.3 0.2 - - - -
544A CYS* 1.3 80.8 - - + +
546A VAL* 1.3 51.7 + - - +
548A MET* 3.0 21.3 + - + +
549A MET* 2.6 36.7 + - - +
573A ILE* 4.8 3.1 - - + -
574A PRO* 5.3 2.8 - - + +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE* 4.4 10.1 - - + -
542A THR* 3.3 15.6 + - + +
543A ILE* 3.3 15.5 - - - +
545A PHE* 1.3 75.2 - - - +
547A PHE* 1.3 66.5 + - + +
549A MET* 3.9 13.3 - - + +
550A ILE* 3.2 27.0 + - - +
1002A D6T 3.5 67.1 - - + -
405B LEU* 6.0 2.5 - - + -
432B PHE* 4.4 11.4 - - + -
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Residues in contact with PHE 547 (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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543A ILE* 3.1 41.0 + - + -
544A CYS* 3.5 8.1 + - - +
545A PHE 3.1 0.6 - - - -
546A VAL* 1.3 85.4 - - + +
548A MET* 1.3 64.8 + - + +
549A MET 3.2 0.2 - - - -
550A ILE* 3.4 18.5 + - + +
551A PHE* 3.2 32.2 - + + -
1002A D6T 5.0 14.6 - + + -
404B VAL* 5.9 3.8 - - + -
405B LEU* 3.8 30.5 - - + -
408B VAL* 4.1 26.2 - - + -
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Residues in contact with MET 548 (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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523A MET* 3.6 33.2 - - + -
544A CYS* 3.1 12.3 + - + +
545A PHE* 3.0 33.1 + - - +
547A PHE* 1.3 76.5 - - + +
549A MET* 1.3 63.0 + - - +
550A ILE 3.4 0.3 + - - -
551A PHE* 3.4 9.7 + - - -
552A SER* 3.5 11.3 + - - -
571A PHE 3.4 20.6 - - - +
572A SER* 3.7 25.1 - - - -
573A ILE* 3.8 22.9 - - + +
574A PRO* 3.6 20.6 - - + +
636A MET* 5.6 2.0 - - + -
640A PHE* 6.1 0.9 - - + -
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Residues in contact with MET 549 (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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431A PHE* 3.6 29.7 - - + -
435A THR* 4.6 6.7 - - + -
439A PHE* 4.5 17.0 - - + -
545A PHE 2.6 19.5 + - - +
546A VAL* 4.0 9.4 - - - +
547A PHE 3.2 0.4 - - - -
548A MET* 1.3 73.8 - - - +
550A ILE* 1.3 57.4 + - - +
552A SER* 2.9 25.9 + - - -
555A LEU* 4.2 18.9 - - + +
574A PRO* 4.9 5.8 - - + +
1002A D6T 3.6 50.0 - - + -
431B PHE* 5.9 5.4 - - + -
432B PHE* 4.3 20.6 - - + -
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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