Contacts of the helix formed by residues 527 - 539 (chain A) in PDB entry 6FWF
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 ALA 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLU* 4.7 14.6 - - + +
502A THR* 5.3 10.1 - - + -
526A ALA* 1.3 76.8 - - - +
528A ALA* 1.3 54.0 + - - +
530A ILE* 3.3 15.2 - - + +
531A PHE* 2.8 39.9 + - - +
566A PRO* 5.4 0.8 - - + +
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Residues in contact with ALA 528 (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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11A LEU* 5.9 4.7 - - + -
454A ILE* 5.7 11.2 - - + -
498A GLU 4.0 18.4 + - - +
499A VAL* 4.1 26.5 - - + +
502A THR* 5.1 2.2 + - - +
526A ALA 3.3 4.9 - - - +
527A ALA* 1.3 78.7 - - - +
529A ALA* 1.3 52.8 + - - +
531A PHE* 3.7 1.7 - - - -
532A MET* 2.8 41.6 + - + +
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.7 2.2 - - + +
11A LEU* 4.9 16.8 - - + +
14A VAL* 4.2 21.7 - - + +
526A ALA* 3.2 17.6 + - - +
528A ALA* 1.3 75.6 - - - +
530A ILE* 1.3 60.8 + - + +
532A MET* 3.6 2.3 - - - -
533A LEU* 2.8 32.4 + - - +
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Residues in contact with ILE 530 (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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526A ALA* 2.8 26.6 + - + +
527A ALA* 3.3 19.7 - - + +
529A ALA* 1.3 74.2 - - + +
531A PHE* 1.3 60.9 + - - +
533A LEU* 3.7 8.8 - - + +
534A GLY* 2.8 27.5 + - - -
562A LEU 5.2 0.5 - - - +
565A VAL* 6.3 0.9 - - + -
566A PRO* 3.8 37.8 - - + +
569A LEU* 6.3 3.1 - - + -
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Residues in contact with PHE 531 (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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494A GLU* 3.7 52.4 - - + +
498A GLU* 3.5 36.1 - - + +
499A VAL* 6.0 0.4 - - + -
527A ALA 2.8 24.1 + - - +
528A ALA* 4.3 2.0 - - - +
530A ILE* 1.3 75.7 - - + +
532A MET* 1.3 59.3 + - + +
534A GLY* 4.4 0.7 - - - +
535A GLY* 2.8 29.4 + - - +
563A GLU* 4.3 23.8 - - + -
566A PRO* 4.5 13.2 - - + -
567A LEU* 3.3 35.9 - - + -
642A TYR* 4.8 4.0 - - - -
1001A HEM 5.1 4.7 - - + -
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Residues in contact with MET 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.8 16.8 - - + -
14A VAL* 4.8 4.0 - - + +
15A LEU* 4.2 23.5 - - + -
18A CYS* 3.6 12.6 - - - +
19A PHE* 6.4 0.7 - - - -
494A GLU 5.5 1.6 - - - +
495A GLY* 4.3 22.4 - - - +
499A VAL* 4.2 24.0 - - + -
528A ALA* 2.8 25.0 + - + +
529A ALA* 3.6 2.9 - - - +
531A PHE* 1.3 72.9 - - + +
533A LEU* 1.3 60.1 + - - +
536A VAL* 3.2 43.5 - - + +
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Residues in contact with LEU 533 (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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14A VAL* 3.7 39.0 - - + +
17A VAL* 4.1 18.6 - - + -
18A CYS* 5.0 3.6 - - + -
21A ILE* 6.2 0.2 - - + -
529A ALA 2.8 19.2 + - - +
530A ILE* 3.8 9.2 - - + +
532A MET* 1.3 78.9 - - - +
534A GLY* 1.3 56.9 + - - +
537A PRO* 3.2 24.3 - - - +
559A PHE* 3.4 23.3 - - + -
562A LEU* 6.2 2.2 - - + -
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Residues in contact with GLY 534 (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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530A ILE 2.8 17.7 + - - -
531A PHE* 5.0 0.4 - - - -
533A LEU* 1.3 77.7 - - - +
535A GLY* 1.3 57.0 + - - +
536A VAL 3.5 0.2 - - - -
538A GLY 3.2 17.7 + - - -
559A PHE* 3.0 31.5 - - - +
562A LEU* 4.5 8.3 - - - -
563A GLU* 3.3 16.2 - - - +
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Residues in contact with GLY 535 (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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490A HIS* 4.5 5.0 + - - +
491A LEU* 3.9 3.9 - - - +
494A GLU* 5.9 5.4 - - - -
531A PHE* 2.8 30.3 + - - +
534A GLY* 1.3 71.6 - - - +
536A VAL* 1.3 59.6 + - - +
537A PRO 3.6 0.2 - - - -
538A GLY 3.8 0.4 - - - -
539A THR* 3.0 28.4 + - - -
563A GLU* 3.5 21.4 - - - +
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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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15A LEU* 5.7 0.2 - - + -
18A CYS* 3.4 24.7 - - + +
19A PHE* 4.2 17.3 - - + -
22A LEU* 3.1 26.9 - - + +
491A LEU* 3.6 15.3 - - + -
532A MET* 3.2 48.6 + - + +
535A GLY* 1.3 75.3 - - - +
537A PRO* 1.3 66.3 - - + +
539A THR* 3.1 25.8 - - - +
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Residues in contact with PRO 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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18A CYS* 3.9 16.4 - - + +
21A ILE* 3.8 23.6 - - + -
22A LEU* 4.4 9.4 - - + -
533A LEU* 3.2 28.3 - - + +
534A GLY 3.7 0.9 - - - +
536A VAL* 1.3 97.2 - - + +
538A GLY* 1.3 60.0 + - - +
539A THR* 3.7 0.4 + - - -
540A LEU* 3.8 16.4 + - - +
555A ILE* 3.8 15.1 - - - +
556A GLY* 4.2 1.2 - - - -
559A PHE* 3.5 33.0 - - + -
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Residues in contact with GLY 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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534A GLY 3.2 15.6 + - - -
536A VAL 3.3 0.4 - - - -
537A PRO* 1.3 73.0 - - - +
539A THR* 1.3 51.2 + - - +
540A LEU 3.0 5.6 - - - -
541A HIS* 2.8 40.2 + - - +
556A GLY 4.0 3.8 - - - +
559A PHE* 3.5 3.0 - - - +
560A SER* 3.7 17.2 - - - -
563A GLU* 3.3 18.8 - - - -
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Residues in contact with THR 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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22A LEU* 4.1 12.6 - - + -
486A TRP* 3.4 15.7 + - + +
487A TRP* 5.5 0.9 - - + +
490A HIS* 3.3 37.7 + - - +
491A LEU* 3.7 20.0 - - + -
535A GLY 3.0 17.3 + - - -
536A VAL 3.1 21.5 - - - +
538A GLY* 1.3 74.4 - - - +
540A LEU* 1.3 66.0 + - + +
541A HIS* 3.1 3.6 + - - -
542A HIS* 2.8 28.9 + - - -
543A LEU* 4.4 3.8 - - - +
563A GLU* 3.6 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
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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