Contacts of the helix formed by residues 544 - 553 (chain M) in PDB entry 6D6Q
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 SER 544 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347M MET* 5.5 2.2 - - - -
542M LYS 4.1 0.8 - - - -
543M MET* 1.3 78.5 - - - +
545M PRO* 1.3 77.2 - - - +
546M THR* 3.0 26.1 + - - +
547M ILE* 3.2 18.0 + - - +
548M GLY* 3.2 4.3 + - - -
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Residues in contact with PRO 545 (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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338M PHE* 5.8 2.3 - - + -
340M GLU* 3.6 24.9 - - - +
343M PHE* 3.8 22.0 - - + -
344M ASN* 4.6 13.7 - - - +
347M MET* 6.0 1.1 - - + -
544M SER* 1.3 88.6 - - - +
546M THR* 1.3 56.4 + - - +
549M LYS* 2.9 35.5 + - + +
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Residues in contact with THR 546 (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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544M SER* 3.0 18.6 + - - +
545M PRO* 1.3 80.3 - - - +
547M ILE* 1.3 72.6 + - + +
549M LYS* 3.8 4.5 - - - +
550M GLN* 2.9 35.3 + - - +
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Residues in contact with ILE 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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511M TRP* 4.1 43.3 - - + +
543M MET* 3.8 25.4 - - + -
544M SER* 3.2 26.9 - - - +
546M THR* 1.3 85.6 - - + +
548M GLY* 1.3 68.6 + - - +
550M GLN* 2.9 37.8 + - - +
551M LEU* 2.9 20.6 + - + +
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Residues in contact with GLY 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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338M PHE* 5.5 3.3 - - - -
343M PHE* 4.5 17.7 - - - -
543M MET* 5.3 5.8 - - - -
544M SER 3.2 8.4 + - - -
545M PRO 4.1 0.7 - - - -
547M ILE* 1.3 85.7 - - - +
549M LYS* 1.3 56.7 + - - +
551M LEU* 3.4 6.2 + - - -
552M LEU* 2.9 43.1 + - - +
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Residues in contact with LYS 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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338M PHE* 4.9 17.3 - - + -
545M PRO* 2.9 23.1 + - + +
546M THR* 3.8 5.2 - - - +
548M GLY* 1.3 72.2 - - - +
550M GLN* 1.3 69.1 + - + +
551M LEU 3.0 4.3 + - - -
552M LEU* 3.2 1.3 + - - -
553M LYS* 2.9 70.9 + - + +
554M GLY* 3.2 5.3 + - - +
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Residues in contact with GLN 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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511M TRP* 6.4 0.2 - - - +
512M ILE 5.4 3.2 + - - -
514M SER* 4.1 9.4 + - - -
546M THR* 2.9 27.8 + - - +
547M ILE* 2.9 35.9 + - - +
549M LYS* 1.3 82.8 - - + +
551M LEU* 1.3 70.6 + - - +
554M GLY* 3.3 23.4 - - - -
555M SER 5.4 0.2 - - - +
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Residues in contact with LEU 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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501M ALA* 4.9 3.8 - - + -
511M TRP* 5.6 4.0 - - + -
512M ILE* 3.3 43.5 - - + +
514M SER* 3.4 24.8 + - - +
517M TYR* 4.1 27.9 - - + -
537M LEU* 4.5 8.3 - - + -
543M MET* 4.5 20.6 - - + -
547M ILE* 2.9 22.8 + - + +
548M GLY* 3.5 4.5 - - - +
549M LYS 3.0 0.2 - - - -
550M GLN* 1.3 87.8 - - - +
552M LEU* 1.3 87.8 + - + +
554M GLY 4.2 0.2 + - - -
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Residues in contact with LEU 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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318M HIS* 4.4 17.4 + - + -
319M TYR 6.5 0.2 - - - -
320M ILE* 5.5 9.0 - - + -
331M VAL* 3.3 37.2 - - + -
332M VAL* 5.0 5.6 - - + -
338M PHE* 4.6 11.4 - - + -
343M PHE* 5.9 2.9 - - + -
514M SER* 4.7 1.2 + - - -
517M TYR* 4.2 25.9 - - + +
518M ILE* 5.2 5.4 - - - +
537M LEU* 4.5 13.5 - - + -
548M GLY* 2.9 38.0 + - - +
549M LYS* 4.3 1.3 - - - +
551M LEU* 1.3 97.3 - - + +
553M LYS* 1.3 62.0 + - + +
554M GLY 4.2 2.6 - - - +
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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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332M VAL* 6.2 3.6 - - + -
336M GLY 5.8 0.7 - - - -
338M PHE* 3.1 55.3 - - + +
549M LYS* 2.9 58.9 + - + +
552M LEU* 1.3 73.8 - - + +
554M GLY* 1.3 70.7 + - - +
555M SER* 3.6 1.4 + - - -
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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