Contacts of the helix formed by residues 546 - 559 (chain M) in PDB entry 2W4G
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 THR 546 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544M LYS 4.6 3.3 + - - -
545M ALA* 1.3 78.8 + - - +
547M ASP* 1.3 79.6 - - + +
548M THR* 3.0 26.5 - - - +
549M SER* 2.9 17.0 + - - -
550M PHE* 2.8 23.4 + - - +
596M LEU* 3.5 8.1 - - - +
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Residues in contact with ASP 547 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546M THR* 1.3 77.6 - - + +
548M THR* 1.3 53.3 + - - +
550M PHE* 3.0 11.3 - - - +
551M LYS* 2.7 37.1 + - - +
592M ILE* 3.7 17.7 - - + +
593M SER* 3.3 8.7 - - - -
594M GLY* 2.9 29.8 + - - -
595M TRP* 4.5 0.7 - - - +
596M LEU* 3.4 32.5 + - - +
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Residues in contact with THR 548 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546M THR* 3.0 17.5 - - + +
547M ASP* 1.3 78.5 - - - +
549M SER* 1.3 64.0 + - - +
551M LYS* 3.3 22.6 + - - +
552M ASN* 2.8 40.7 + - - +
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Residues in contact with SER 549 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539M GLU* 2.8 30.2 + - - +
545M ALA* 3.6 3.4 - - - +
546M THR* 2.9 31.1 + - - -
548M THR* 1.3 86.5 - - - +
550M PHE* 1.3 80.1 + - - +
552M ASN* 3.0 16.3 + - - +
553M LYS* 3.1 12.7 + - - +
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Residues in contact with PHE 550 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532M ILE* 4.4 3.1 - - + -
535M ILE* 3.9 20.4 - - + -
536M LEU* 3.2 53.8 - - + -
539M GLU* 4.1 10.5 - - + -
546M THR 2.8 9.7 + - - +
547M ASP* 3.0 8.5 - - - +
549M SER* 1.3 78.9 + - - +
551M LYS* 1.3 64.9 + - - +
553M LYS* 3.0 5.5 + - - +
554M LEU* 2.9 40.7 + - + +
592M ILE* 3.0 40.4 - - + -
595M TRP* 4.1 16.2 - + + -
596M LEU* 3.8 19.1 - - + -
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Residues in contact with LYS 551 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547M ASP 2.7 19.2 + - - +
548M THR* 3.5 24.3 + - - +
550M PHE* 1.3 76.5 - - - +
552M ASN* 1.3 69.4 + - - +
554M LEU* 2.7 32.0 + - + +
555M TYR* 3.0 41.6 + - + +
578M HIS* 3.8 27.0 + - + +
592M ILE* 4.4 18.4 - - + -
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Residues in contact with ASN 552 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548M THR* 2.8 36.2 + - - +
549M SER* 3.0 9.7 + - - +
551M LYS* 1.3 87.7 - - - +
553M LYS* 1.3 63.6 + - + +
555M TYR* 2.9 11.6 + - - -
556M ASP* 2.9 38.9 + - - +
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Residues in contact with LYS 553 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535M ILE* 3.9 19.1 - - + +
538M GLU* 5.0 8.8 + - - +
539M GLU* 3.0 45.6 + - - +
542M PHE* 4.1 24.4 - - - -
549M SER 3.1 8.0 + - - +
550M PHE* 3.0 10.3 + - - +
552M ASN* 1.3 79.2 - - + +
554M LEU* 1.3 64.5 + - - +
556M ASP* 4.4 5.0 - - + +
557M GLN* 3.6 21.7 + - - +
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Residues in contact with LEU 554 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532M ILE* 4.1 23.1 - - + -
535M ILE* 3.4 35.7 - - + -
550M PHE* 2.9 36.1 + - + +
551M LYS* 2.7 14.8 + - + +
553M LYS* 1.3 79.4 - - - +
555M TYR* 1.3 62.1 + - + +
558M HIS* 3.1 30.7 + - + +
565M PHE* 4.1 18.2 - - + -
579M PHE* 3.9 31.4 - - + -
592M ILE* 4.4 5.2 - - + -
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Residues in contact with TYR 555 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551M LYS* 3.0 52.2 + - + +
552M ASN* 2.9 15.7 + - - +
554M LEU* 1.3 75.1 - - + +
556M ASP* 1.3 59.1 + - - +
557M GLN 2.7 16.5 + - - -
558M HIS 2.7 0.3 + - - -
559M LEU* 2.7 62.4 + - + +
565M PHE* 3.8 17.5 - + - -
567M LYS* 4.4 12.6 - - + +
568M PRO* 4.6 4.3 - - - +
578M HIS* 2.9 30.3 + - - -
579M PHE* 4.9 0.4 - - + -
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Residues in contact with ASP 556 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552M ASN* 2.9 27.0 + - - +
553M LYS* 4.4 4.9 - - + +
555M TYR* 1.3 78.9 - - - +
557M GLN* 1.3 58.9 + - + +
559M LEU 5.0 3.7 - - - +
561M LYS* 5.9 1.6 - - - -
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Residues in contact with GLN 557 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530M MET* 3.6 41.2 - - - +
535M ILE* 4.2 5.4 - - + -
553M LYS 3.6 16.6 + - - +
554M LEU 4.2 0.4 - - - +
555M TYR 2.7 5.1 + - - -
556M ASP* 1.3 79.1 - - + +
558M HIS* 1.3 83.0 + - + +
559M LEU 3.8 0.2 - - - -
561M LYS* 4.2 33.5 - - - +
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Residues in contact with HIS 558 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525M LEU* 3.7 25.1 - - + +
530M MET* 2.7 30.8 + - + -
531M GLY* 3.6 16.3 - - - -
532M ILE* 4.1 6.3 + - + -
535M ILE* 3.8 8.9 - - + +
554M LEU* 3.1 27.1 + - + +
555M TYR 2.7 4.6 + - - -
557M GLN* 1.3 91.3 + - + +
559M LEU* 1.3 63.4 + - - +
560M GLY 3.3 0.2 + - - -
561M LYS* 3.1 2.4 + - - -
562M SER* 2.8 39.6 + - - +
565M PHE* 3.7 25.9 - + + -
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Residues in contact with LEU 559 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555M TYR* 2.7 53.6 + - + +
556M ASP 5.0 3.8 - - - +
558M HIS* 1.3 72.8 - - - +
560M GLY* 1.3 68.3 + - - +
561M LYS* 3.0 8.1 + - - +
565M PHE* 3.6 20.6 - - + +
566M GLN* 5.4 0.7 - - - -
567M LYS* 4.3 33.4 - - + +
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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