Contacts of the helix formed by residues 531 - 539 (chain C) in PDB entry 3H52
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 531 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B GLU* 3.7 8.5 - - - +
699B LYS* 3.5 28.5 - - - +
530C PRO* 1.3 78.7 - - - +
532C LEU* 1.3 76.0 + - + +
533C VAL* 3.8 6.7 - - + +
534C SER* 3.1 16.0 + - - -
535C LEU* 2.9 23.0 + - - +
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Residues in contact with LEU 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PRO* 3.6 26.9 - - + -
692B THR* 3.6 28.3 - - + -
693B TYR* 3.6 42.8 - - + +
696B GLU* 3.3 29.6 - - + +
531C THR* 1.3 74.6 - - + +
533C VAL* 1.3 64.8 + - - +
535C LEU* 2.9 13.8 + - + +
536C LEU* 2.8 24.1 + - + +
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Residues in contact with VAL 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B GLU* 3.4 47.3 - - + +
664B LEU* 4.4 4.8 - - + +
665B CYS* 4.0 15.7 - - - -
696B GLU* 3.1 39.3 + - + +
699B LYS* 5.7 1.3 - - + -
700B ALA* 5.1 4.5 - - + +
703B LYS* 5.5 0.2 - - - +
531C THR* 3.8 7.4 - - + +
532C LEU* 1.3 78.0 - - - +
534C SER* 1.3 65.8 + - - +
536C LEU* 3.2 12.1 + - - +
537C GLU* 3.1 21.6 + - + +
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Residues in contact with SER 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C PRO* 3.7 12.9 - - - +
531C THR* 3.1 29.0 + - - -
533C VAL* 1.3 81.5 - - - +
535C LEU* 1.3 60.8 + - - +
537C GLU* 3.1 20.6 + - - +
538C VAL* 2.9 26.7 + - - +
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Residues in contact with LEU 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PRO* 4.4 25.1 - - + -
529C THR* 6.3 0.2 - - - -
530C PRO* 3.4 44.9 - - + +
531C THR 2.9 17.9 + - - +
532C LEU* 3.2 13.2 - - + +
534C SER* 1.3 78.1 - - - +
536C LEU* 1.3 61.1 + - - +
538C VAL* 3.1 20.7 + - + +
539C ILE* 3.1 24.4 + - + +
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Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B TRP* 5.1 4.2 + - - +
581B ILE* 4.4 6.7 - - + -
582B PRO* 4.1 21.5 - - + -
664B LEU* 3.7 36.5 - - + +
665B CYS* 4.4 12.8 - - - +
668B THR* 3.3 25.8 - - - +
693B TYR* 3.8 32.1 - - + +
696B GLU* 5.1 0.4 - - + -
532C LEU* 2.8 23.2 + - + +
533C VAL* 3.2 10.5 + - - +
535C LEU* 1.3 70.8 - - - +
537C GLU* 1.3 60.4 + - - +
539C ILE* 4.0 13.9 - - + +
540C GLU* 3.6 14.9 + - - +
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Residues in contact with GLU 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B TYR* 3.5 31.4 + - + +
661B GLU* 5.6 5.8 - - + +
664B LEU* 3.5 15.5 - - + +
533C VAL* 3.1 9.7 + - + +
534C SER* 3.1 18.1 + - - +
536C LEU* 1.3 76.5 - - - +
538C VAL* 1.3 67.4 + - + +
539C ILE 3.5 0.2 + - - -
540C GLU* 3.6 16.2 + - - +
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C PRO* 5.9 2.0 - - + -
534C SER* 2.9 25.4 - - - +
535C LEU* 3.1 15.8 + - + +
537C GLU* 1.3 81.7 - - + +
539C ILE* 1.3 64.6 + - + +
540C GLU 3.3 6.7 + - - +
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Residues in contact with ILE 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B TRP* 3.5 16.7 - - + +
580B ALA* 3.1 51.4 - - + +
581B ILE* 3.7 18.8 - - + +
582B PRO* 4.4 3.1 - - + -
535C LEU* 3.4 19.7 - - + +
536C LEU* 4.0 16.6 - - + +
538C VAL* 1.3 82.2 - - + +
540C GLU* 1.3 64.1 + - - +
541C PRO* 3.2 11.3 - - - +
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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