Contacts of the helix formed by residues 551 - 556 (chain E) in PDB entry 6DWZ
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 TYR 551 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523E GLU* 3.1 26.0 - - + +
526E PHE* 3.4 29.0 + + + -
527E TYR* 3.1 25.6 - + + -
530E GLU* 2.6 51.1 + - + +
543E TRP* 4.9 7.9 - + - -
544E TRP* 4.7 4.9 - + + -
547E ASN* 4.3 6.1 - - + -
550E LYS* 1.3 102.0 - - + +
552E PRO* 1.3 57.8 - - - +
553E LYS 3.6 1.3 - - - -
554E LEU* 2.9 28.9 + - + -
555E SER* 2.3 43.3 + - - +
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Residues in contact with PRO 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E VAL* 5.9 7.0 - - + +
523E GLU* 3.1 16.2 - - + +
549E LYS* 2.9 36.1 - - + +
550E LYS 3.7 3.6 - - - +
551E TYR* 1.3 85.9 - - - +
553E LYS* 1.3 63.8 + - + +
554E LEU 3.2 1.0 + - - -
555E SER* 3.5 9.5 + - - +
556E LYS* 4.3 8.7 + - - +
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Residues in contact with LYS 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E MET* 3.2 39.1 - - + +
459E GLU* 5.5 6.1 + - - +
462E GLU* 3.7 37.1 - - - +
520E PRO* 4.6 19.8 - - + +
523E GLU* 3.2 17.9 + - - +
552E PRO* 1.3 80.2 - - + +
554E LEU* 1.3 58.1 + - - +
556E LYS* 5.2 1.0 - - - +
557E LEU* 5.0 4.9 + - - +
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Residues in contact with LEU 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435E PHE* 5.0 17.3 - - + -
454E CYS* 5.3 5.4 - - + -
455E LEU* 5.5 0.4 - - + -
458E MET* 3.6 29.2 - - + +
523E GLU* 3.7 7.1 + - + +
524E PHE* 4.4 19.3 - - + +
527E TYR* 3.7 27.4 - - + -
544E TRP* 3.5 27.4 - - + -
551E TYR* 2.9 28.4 + - + +
553E LYS* 1.3 76.7 - - - +
555E SER* 1.3 50.1 + - - +
556E LYS 2.7 3.0 + - - -
557E LEU* 2.4 41.3 + - + +
558E ALA 3.7 2.1 + - - -
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Residues in contact with SER 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E TRP* 3.3 26.0 - - - +
547E ASN 4.0 1.0 + - - -
548E SER* 3.3 16.1 - - - -
549E LYS* 2.4 36.0 + - - -
551E TYR* 2.3 38.3 + - - +
552E PRO 3.5 4.6 + - - -
554E LEU* 1.3 64.4 - - - +
556E LYS* 1.3 60.8 + - - +
559E LEU* 3.0 25.9 + - - +
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Residues in contact with LYS 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E LYS* 3.9 32.2 - - - +
199E HIS* 5.8 0.2 - - - +
552E PRO 4.3 7.3 + - - +
553E LYS 5.9 1.1 - - - +
554E LEU 2.7 5.3 + - - -
555E SER* 1.3 75.9 - - - +
557E LEU* 1.3 59.6 + - - +
559E LEU* 3.0 31.5 - - + +
560E SER* 3.0 25.5 + - - -
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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