Contacts of the helix formed by residues 542 - 557 (chain T) in PDB entry 6FF7
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 ASN 542 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1409A GLU 6.1 1.1 - - - +
498T ALA 5.0 0.2 - - - -
501T ARG 5.6 6.1 - - - +
540T GLU 2.8 8.2 + - - +
541T THR* 1.3 80.1 - - - +
543T LYS* 1.3 59.4 + - - +
544T LEU 2.9 0.7 - - - -
545T ARG* 2.6 29.2 + - - +
546T ASN* 3.0 11.5 + - - +
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Residues in contact with LYS 543 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498T ALA* 3.6 35.2 + - + +
499T GLN* 6.3 0.2 - - + -
539T LEU* 3.6 26.2 - - + -
540T GLU 4.3 2.3 + - - +
542T ASN* 1.3 78.2 - - - +
544T LEU* 1.3 56.7 + - - +
546T ASN* 3.8 1.5 - - - +
547T VAL* 2.9 33.9 + - - +
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Residues in contact with LEU 544 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536T ILE* 5.4 4.7 - - + +
539T LEU* 4.2 7.9 - - - +
540T GLU* 4.0 10.3 - - + +
541T THR* 3.7 22.1 - - - +
542T ASN 2.9 1.0 + - - +
543T LYS* 1.3 80.0 - - - +
545T ARG* 1.3 56.0 + - - +
547T VAL* 4.0 2.9 - - - +
548T ALA* 2.9 30.3 + - - +
578T SER* 5.7 4.7 - - - +
581T ILE 6.0 0.9 - - - +
582T PHE* 5.4 14.3 - - + +
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Residues in contact with ARG 545 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503T TYR* 5.8 0.2 - - - -
541T THR 4.7 5.3 - - - +
542T ASN* 2.6 21.0 + - - +
544T LEU* 1.3 72.0 - - - +
546T ASN* 1.3 64.5 + - - +
548T ALA* 3.2 5.3 + - - +
549T LYS* 2.9 27.0 + - - +
585T ILE* 5.6 10.1 - - + -
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Residues in contact with ASN 546 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497T CYS* 3.9 16.3 - - - +
498T ALA* 3.6 26.5 - - - +
500T GLN 5.5 2.9 - - - +
501T ARG 5.6 3.4 - - - +
503T TYR* 4.4 27.0 - - + +
542T ASN 3.0 8.9 + - - +
543T LYS 3.9 2.2 - - - +
545T ARG* 1.3 76.8 - - - +
547T VAL* 1.3 56.7 + - - +
549T LYS* 3.9 2.0 - - - +
550T MET* 3.0 26.2 + - - +
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Residues in contact with VAL 547 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494T LEU 6.0 0.7 - - - +
497T CYS* 6.6 0.2 - - - -
498T ALA* 5.0 11.4 - - + +
543T LYS 2.9 18.2 + - - +
544T LEU* 4.2 3.1 - - - +
546T ASN* 1.3 75.3 - - - +
548T ALA* 1.3 67.7 + - - +
550T MET* 2.9 22.8 + - + +
551T PHE* 2.9 10.0 + - - +
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Residues in contact with ALA 548 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544T LEU 2.9 20.5 + - - +
545T ARG* 3.2 5.8 + - - +
547T VAL* 1.3 76.2 - - - +
549T LYS* 1.3 58.1 + - - +
551T PHE* 2.8 24.3 + - - +
552T ALA* 2.9 13.5 + - - +
582T PHE* 3.9 25.1 - - + +
585T ILE* 4.9 5.8 - - + -
586T PHE* 4.5 16.9 - - + +
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Residues in contact with LYS 549 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503T TYR* 5.0 11.7 - - + -
545T ARG 2.9 18.6 + - - +
546T ASN* 4.2 4.5 - - - +
548T ALA* 1.3 73.6 - - - +
550T MET* 1.3 62.9 + - - +
552T ALA* 4.0 8.5 - - - +
553T HIS* 2.9 26.0 + - - +
585T ILE 5.6 0.8 + - - -
589T GLU* 5.3 13.2 - - + -
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Residues in contact with MET 550 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497T CYS* 5.5 11.0 - - + -
507T PHE* 6.1 3.4 - - + -
508T GLY* 4.9 9.7 - - - +
546T ASN 3.0 18.1 + - - +
547T VAL* 2.9 19.2 + - + +
549T LYS* 1.3 79.0 - - - +
551T PHE* 1.3 58.9 + - - +
553T HIS* 3.5 5.4 + - - +
554T LEU* 3.3 16.5 + - - +
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Residues in contact with PHE 551 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529T PHE* 5.8 8.1 - - + -
547T VAL 2.9 7.8 + - - +
548T ALA* 2.8 15.4 + - - +
550T MET* 1.3 68.7 - - - +
552T ALA* 1.3 66.1 + - - +
553T HIS 3.0 1.8 - - - -
554T LEU* 2.9 17.2 + - - +
555T LEU* 2.9 15.0 + - - +
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Residues in contact with ALA 552 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548T ALA 2.9 13.8 + - - +
549T LYS* 4.0 8.7 - - - +
551T PHE* 1.3 75.6 - - - +
553T HIS* 1.3 64.2 + - - +
555T LEU* 3.4 6.5 + - - +
556T TYR* 2.9 25.6 + - - +
586T PHE* 3.9 23.8 - - + +
589T GLU* 4.9 3.6 - - + +
590T LEU* 4.0 22.4 - - + +
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Residues in contact with HIS 553 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505T LYS* 6.5 0.9 - - - -
508T GLY* 4.5 20.2 - - - +
549T LYS 2.9 19.2 + - - +
550T MET* 3.7 5.8 - - - +
551T PHE 3.0 0.2 - - - -
552T ALA* 1.3 76.2 - - - +
554T LEU* 1.3 63.0 + - - +
556T TYR* 3.5 5.5 + - - +
557T THR* 3.1 25.8 + - - -
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Residues in contact with LEU 554 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508T GLY* 5.3 8.2 + - - +
511T ALA* 6.4 2.2 - - + -
512T GLY* 6.1 6.3 - - - +
550T MET 3.3 9.5 + - - +
551T PHE* 2.9 10.5 + - - +
553T HIS* 1.3 78.1 - - - +
555T LEU* 1.3 50.4 + - - +
557T THR* 3.0 5.0 + - - -
558T ASP 2.5 47.7 + - - +
559T SER* 5.0 2.7 - - - +
560T LEU* 4.4 12.8 - - + -
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Residues in contact with LEU 555 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551T PHE 2.9 11.3 + - - +
552T ALA* 3.8 9.6 - - - +
554T LEU* 1.3 73.9 - - - +
556T TYR* 1.3 57.9 + - - +
558T ASP* 2.6 27.2 + - - +
560T LEU* 4.8 8.8 - - - +
562T TRP* 6.4 2.2 - - - -
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Residues in contact with TYR 556 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552T ALA 2.9 18.2 + - - +
553T HIS* 3.9 5.4 - - - +
555T LEU* 1.3 78.6 - - - +
557T THR* 1.3 57.5 + - - +
558T ASP* 3.3 2.8 + - - +
590T LEU* 5.8 4.3 - - + +
593T TYR* 4.1 25.1 - - + -
594T MET* 5.7 3.8 - - + +
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Residues in contact with THR 557 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209A HIS* 5.7 9.6 - - - -
508T GLY 5.4 7.0 - - - -
553T HIS 3.1 15.6 + - - -
554T LEU* 3.0 4.4 + - - -
556T TYR* 1.3 75.7 - - - +
558T ASP* 1.3 72.1 + - - +
559T SER* 3.3 7.1 + - - -
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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