Contacts of the helix formed by residues 544 - 559 (chain F) in PDB entry 2AJQ
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 GLY 544 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534F ASP 4.1 5.2 - - - -
535F GLU* 4.4 8.5 - - - -
538F GLY* 3.4 9.7 - - - -
539F GLN* 4.9 1.3 - - - -
543F ALA* 1.3 83.1 - - - +
545F LYS* 1.3 68.2 + - - -
546F GLU 3.3 2.9 - - - -
547F ARG* 3.1 4.0 + - - +
548F GLY 3.0 16.8 + - - -
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Residues in contact with LYS 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ASP* 3.8 26.3 - - + +
535F GLU* 4.1 13.7 - - + +
544F GLY* 1.3 69.6 - - - -
546F GLU* 1.3 69.7 + - - +
548F GLY* 2.9 10.9 + - - -
549F LYS* 3.1 39.5 + - - +
952Z T 3.7 33.4 + - - +
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Residues in contact with GLU 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544F GLY 3.3 1.0 - - - -
545F LYS* 1.3 87.9 - - - +
547F ARG* 1.3 62.6 + - - +
548F GLY 3.2 0.7 + - - -
549F LYS* 3.7 3.4 + - - +
550F GLU* 3.3 26.6 + - + +
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Residues in contact with ARG 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F GLU* 3.9 15.8 + - - +
515F LEU* 5.2 3.2 - - - +
516F PRO* 5.5 2.8 - - - +
538F GLY* 4.3 2.9 - - - -
541F VAL* 3.7 32.1 - - + +
543F ALA* 3.5 24.0 - - + -
544F GLY 3.1 5.9 + - - +
546F GLU* 1.3 78.4 - - - +
548F GLY* 1.3 56.9 + - - +
550F GLU* 3.3 34.8 + - - +
551F LEU* 2.8 70.1 + - + +
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Residues in contact with GLY 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ASP* 3.2 30.3 - - - -
537F ILE* 4.2 6.3 - - - -
538F GLY* 3.9 8.9 - - - -
544F GLY 3.0 5.7 + - - -
545F LYS 2.9 6.7 + - - -
547F ARG* 1.3 72.8 - - - +
549F LYS* 1.3 54.1 - - - -
550F GLU 2.9 3.4 - - - -
551F LEU* 2.7 24.8 + - - +
552F LYS* 3.0 14.7 + - - +
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Residues in contact with LYS 549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ASP* 3.2 35.2 + - + +
545F LYS* 3.1 33.1 + - - +
546F GLU* 4.4 3.6 - - - +
548F GLY* 1.3 72.1 - - - +
550F GLU* 1.3 60.9 + - - +
552F LYS* 4.0 4.0 - - - +
553F LYS* 3.2 26.0 + - - +
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Residues in contact with GLU 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546F GLU* 3.3 20.5 + - + +
547F ARG* 3.3 38.6 + - - +
548F GLY 2.9 0.8 - - - -
549F LYS* 1.3 78.9 - - - +
551F LEU* 1.3 64.2 + - - +
553F LYS* 4.2 3.2 - - - +
554F LYS* 3.2 29.3 + - + +
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Residues in contact with LEU 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513F ALA* 3.3 27.7 - - + +
515F LEU* 3.7 27.4 - - + -
524F PHE* 4.2 13.9 - - + -
537F ILE* 3.9 31.0 - - + +
540F ILE* 5.6 0.7 - - + -
541F VAL* 4.5 7.2 - - + -
547F ARG* 2.8 55.6 + - + +
548F GLY 2.7 11.2 + - - +
550F GLU* 1.3 71.8 - - - +
552F LYS* 1.3 60.3 + - - +
554F LYS* 3.6 3.7 + - + +
555F PHE* 3.2 22.5 + - - +
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Residues in contact with LYS 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524F PHE* 4.7 2.5 - - + -
528F PHE* 3.9 31.9 - - + -
532F ALA 2.7 29.6 + - - -
533F GLY* 3.5 9.2 - - - -
534F ASP* 3.3 26.8 + - - +
537F ILE* 3.7 25.4 - - + -
548F GLY 3.0 14.1 + - - +
549F LYS* 4.2 4.0 - - - +
551F LEU* 1.3 73.6 - - - +
553F LYS* 1.3 61.7 + - - +
555F PHE* 3.1 8.4 + - - +
556F LEU* 2.9 38.2 + - + +
566F ARG* 5.8 1.6 - - - +
953Z G 5.3 1.2 + - - -
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Residues in contact with LYS 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549F LYS 3.2 17.3 + - - +
550F GLU* 4.2 4.3 - - - +
552F LYS* 1.3 79.0 - - - +
554F LYS* 1.3 61.9 + - - +
556F LEU* 3.9 10.2 - - + +
557F GLU* 3.0 36.6 + - + +
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Residues in contact with LYS 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F ALA 3.8 7.9 - - - +
513F ALA 4.6 8.1 - - - +
514F GLU* 3.4 38.1 + - + +
550F GLU* 3.2 22.9 + - + +
551F LEU* 3.8 5.8 - - + +
552F LYS 3.2 0.8 - - - -
553F LYS* 1.3 75.6 - - - +
555F PHE* 1.3 64.7 + - - +
557F GLU* 3.1 33.2 + - - +
558F ASN* 3.0 39.3 + - - +
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Residues in contact with PHE 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ASN* 3.9 31.6 - - + -
512F ALA* 3.8 15.2 + - + -
513F ALA* 3.8 13.0 - - + +
524F PHE* 3.5 23.8 - + + -
525F ILE* 3.4 20.6 - - + -
528F PHE* 3.4 39.9 - + - -
551F LEU 3.2 11.2 + - - +
552F LYS 3.1 8.0 + - - +
554F LYS* 1.3 80.9 - - - +
556F LEU* 1.3 57.8 - - + +
558F ASN* 3.4 1.7 + - - +
559F THR* 2.8 45.2 + - + -
562F ILE* 3.5 31.6 - - + -
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Residues in contact with LEU 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528F PHE* 3.4 29.6 - - + -
552F LYS* 2.9 24.9 + - + +
553F LYS* 4.0 7.9 - - + +
555F PHE* 1.3 73.1 - - + +
557F GLU* 1.3 65.6 + - - +
559F THR 3.4 10.1 + - - +
560F PRO* 3.4 15.9 - - - +
562F ILE* 4.1 7.0 - - + -
563F ALA* 4.0 36.8 - - + +
566F ARG* 3.2 25.4 - - - +
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Residues in contact with GLU 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553F LYS* 3.0 34.6 + - + +
554F LYS* 3.4 31.0 + - - +
556F LEU* 1.3 76.8 - - - +
558F ASN* 1.3 64.9 + - - +
559F THR 3.6 0.2 + - - -
560F PRO* 3.6 14.4 - - - +
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Residues in contact with ASN 558 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511F ILE* 4.5 7.5 + - - +
512F ALA* 3.7 40.3 + - + +
514F GLU* 5.1 4.2 + - - -
554F LYS* 3.0 36.2 + - - +
555F PHE 3.9 0.9 - - - +
557F GLU* 1.3 81.2 - - - +
559F THR* 1.3 58.2 + - - +
560F PRO* 3.3 9.7 - - - +
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Residues in contact with THR 559 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488F MET* 4.1 13.5 - - + -
496F TYR* 4.4 14.8 - - + -
508F LYS* 6.4 0.7 - - + -
509F ASN* 5.7 0.2 - - - +
512F ALA* 3.9 8.1 - - - +
555F PHE* 2.8 33.5 + - + -
556F LEU* 3.5 6.3 - - - +
557F GLU 3.4 0.4 - - - -
558F ASN* 1.3 80.6 + - - +
560F PRO* 1.3 54.5 - - - +
561F ALA* 3.1 3.1 - - + -
562F ILE* 2.8 55.8 + - + +
563F ALA 3.4 5.9 + - - -
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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