Contacts of the helix formed by residues 562 - 566 (chain A) in PDB entry 1MUK
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 ALA 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A SER* 1.3 80.1 - - - +
563A VAL* 1.3 65.4 - - - +
564A ILE* 3.5 28.5 - - + -
565A GLU* 3.1 27.5 + - - +
566A LYS* 3.5 12.2 - - - +
830A HIS* 6.3 1.3 - - + +
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Residues in contact with VAL 563 (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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561A SER 3.9 1.5 + - - +
562A ALA* 1.3 72.2 - - - +
564A ILE* 1.3 63.2 + - - +
565A GLU 3.1 1.6 + - - -
566A LYS* 3.1 22.8 + - + +
567A VAL 4.8 0.2 + - - -
568A ILE* 3.6 35.2 - - + +
784A LEU* 4.2 17.9 - - + -
791A ARG* 3.7 29.4 - - - +
798A HIS* 5.1 13.0 - - + -
830A HIS* 4.8 22.7 - - + +
831A ASP* 4.8 7.9 - - - +
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Residues in contact with ILE 564 (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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562A ALA* 3.5 21.5 - - + -
563A VAL* 1.3 77.7 - - + +
565A GLU* 1.3 67.4 + - + +
566A LYS 3.6 0.4 + - - -
567A VAL 5.1 1.2 + - - -
568A ILE* 5.4 4.0 - - - -
830A HIS* 3.6 33.4 - - + +
1102A THR* 2.8 29.4 + - - +
1182A ASP* 3.3 32.8 - - - +
1185A MET* 3.5 41.0 - - + +
1186A SER* 5.3 3.6 - - - +
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Residues in contact with GLU 565 (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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558A THR 5.3 0.3 - - - +
559A SER* 2.9 19.2 + - - -
560A GLY* 3.5 24.5 + - - +
561A SER 3.4 15.9 + - - -
562A ALA* 3.1 30.5 + - + +
564A ILE* 1.3 80.4 - - + +
566A LYS* 1.3 57.4 + - - +
567A VAL* 3.4 12.0 + - - +
1101A SER* 5.8 0.2 + - - -
1102A THR* 3.7 11.7 - - - +
1103A ARG* 5.1 17.1 + - + +
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Residues in contact with LYS 566 (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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559A SER* 3.1 17.5 - - - +
560A GLY 3.8 16.4 - - - -
561A SER* 3.6 28.1 + - - +
562A ALA 3.5 11.4 - - - +
563A VAL* 3.1 8.2 + - - +
564A ILE 3.6 0.4 - - - -
565A GLU* 1.3 75.9 - - - +
567A VAL* 1.3 71.4 + - - +
568A ILE* 3.2 3.3 + - - -
781A TYR* 5.2 3.3 - - - +
782A LEU* 2.9 48.0 + - + +
783A LYS* 3.6 18.0 - - - +
784A LEU* 3.7 33.3 - - + +
786A PHE* 5.6 1.0 - - - -
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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