Contacts of the helix formed by residues 544 - 554 (chain A) in PDB entry 6C90
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A PHE* 3.3 8.1 - - - -
543A MET* 1.3 74.9 - - - +
545A PRO* 1.3 68.3 - - - +
546A THR* 3.6 8.2 + - - -
547A ILE* 3.3 32.0 + - - +
548A GLY 2.9 23.4 + - - -
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Residues in contact with PRO 545 (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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338A PHE* 4.3 6.6 - - + -
340A GLU* 3.9 26.2 - - + +
343A PHE* 3.5 20.2 - - + -
344A ASN* 3.5 27.1 - - - +
543A MET 4.4 0.9 - - - +
544A SER* 1.3 88.0 - - - +
546A THR* 1.3 57.7 + - - +
549A LYS* 2.8 31.7 + - - +
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Residues in contact with THR 546 (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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544A SER* 3.2 9.4 + - - -
545A PRO* 1.3 78.4 - - - +
547A ILE* 1.3 62.9 + - + +
549A LYS* 3.1 7.2 + - - +
550A GLN* 2.9 50.2 + - + +
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Residues in contact with ILE 547 (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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511A TRP* 3.9 35.7 - - + +
543A MET* 3.2 40.4 - - + -
544A SER* 3.3 23.7 + - - +
546A THR* 1.3 79.6 - - + +
548A GLY* 1.3 57.8 + - - +
550A GLN* 3.6 23.0 - - - +
551A LEU* 2.8 32.7 + - + +
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Residues in contact with GLY 548 (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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338A PHE* 4.4 7.0 - - - -
343A PHE* 4.0 11.2 - - - -
543A MET* 3.9 17.9 - - - -
544A SER 2.9 19.2 + - - -
545A PRO 3.7 1.3 - - - -
547A ILE* 1.3 79.9 - - - +
549A LYS* 1.3 56.2 + - - +
551A LEU* 4.5 1.1 - - - -
552A LEU* 3.0 36.2 + - - +
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Residues in contact with LYS 549 (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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338A PHE* 4.3 31.3 - - + -
545A PRO 2.8 18.9 + - - +
546A THR* 3.6 4.7 - - - +
548A GLY* 1.3 73.1 - - - +
550A GLN* 1.3 60.3 + - - +
553A LYS* 2.6 76.2 + - + +
554A GLY 3.2 0.5 + - - -
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Residues in contact with GLN 550 (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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514A SER* 3.5 7.9 - - - -
546A THR* 2.9 36.5 + - + +
547A ILE* 3.6 24.2 - - - +
549A LYS* 1.3 77.4 - - + +
551A LEU* 1.3 58.5 + - - +
554A GLY* 2.7 33.2 + - - +
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Residues in contact with LEU 551 (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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501A ALA* 4.8 2.5 - - + +
511A TRP* 4.7 16.2 - - + -
512A ILE* 3.2 48.0 - - + +
513A SER 3.8 4.0 - - - +
514A SER* 3.9 14.0 - - - +
517A TYR* 3.7 26.6 - - + -
518A ILE* 5.8 0.7 - - - +
537A LEU* 4.1 22.0 - - + -
543A MET* 4.3 14.4 - - + -
547A ILE* 2.8 21.7 + - + +
548A GLY* 3.9 4.0 - - - +
550A GLN* 1.3 75.8 - - - +
552A LEU* 1.3 69.7 + - + +
553A LYS 3.6 0.2 + - - -
554A GLY 4.3 0.9 + - - +
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Residues in contact with LEU 552 (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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318A HIS* 4.2 14.9 - - + +
319A TYR 5.6 1.3 - - - +
320A ILE* 4.7 11.2 - - + -
331A VAL* 3.2 36.6 - - + -
332A VAL* 3.9 26.5 - - + +
338A PHE* 5.1 4.5 - - + -
343A PHE* 5.7 0.2 - - + -
517A TYR* 4.1 27.3 - - + +
537A LEU* 3.8 26.7 - - + -
543A MET* 5.4 1.1 - - + -
548A GLY* 3.0 26.4 + - - +
549A LYS* 5.0 1.3 - - - -
551A LEU* 1.3 87.8 - - + +
553A LYS* 1.3 58.7 + - + +
554A GLY 5.2 0.4 - - - -
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Residues in contact with LYS 553 (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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332A VAL* 5.6 5.2 - - + -
336A GLY 3.2 26.3 + - - +
337A ASP* 4.3 5.9 + - - +
338A PHE* 3.9 20.9 - - + +
549A LYS* 2.6 57.1 + - + +
552A LEU* 1.3 75.8 - - + +
554A GLY* 1.3 65.7 + - - +
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Residues in contact with GLY 554 (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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514A SER* 3.7 7.4 - - - -
518A ILE* 3.6 14.9 - - - +
549A LYS 3.2 2.6 + - - -
550A GLN* 2.7 33.0 + - - -
551A LEU 4.3 0.9 + - - +
552A LEU 3.9 0.5 - - - -
553A LYS* 1.3 78.2 - - - +
555A SER* 1.3 65.7 + - - -
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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