Contacts of the helix formed by residues 531 - 538 (chain E) in PDB entry 6M04
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 531 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505E ILE 4.5 6.3 - - - +
506E PRO* 3.8 11.0 - - + +
507E ALA* 3.7 17.9 - - - +
528E GLU* 5.2 9.2 - - + -
529E GLN 3.2 1.8 - - - +
530E THR* 1.3 78.3 - - + +
532E PHE* 1.3 62.9 + - - +
533E SER 3.3 2.9 - - - -
534E PHE* 3.2 38.3 - - + -
535E LEU* 3.3 20.2 - - + +
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Residues in contact with PHE 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528E GLU* 4.6 15.9 - - - +
529E GLN* 3.7 17.9 + - - +
530E THR 3.4 2.4 - - - -
531E ALA* 1.3 77.6 - - - +
533E SER* 1.3 63.6 + - - +
534E PHE 3.7 0.2 - - - -
535E LEU* 3.3 23.4 - - + +
536E ARG* 2.9 54.7 + - + +
555E TRP* 4.2 22.7 - - + -
558E LEU* 3.2 44.2 - - + -
559E LEU* 3.9 9.4 - - + -
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Residues in contact with SER 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692D HIS* 6.4 0.7 - - - -
530E THR 4.9 3.0 + - - -
531E ALA 3.3 1.4 + - - -
532E PHE* 1.3 82.5 - - - +
534E PHE* 1.3 62.7 + - - +
536E ARG* 3.0 19.6 + - - +
537E ASP* 2.9 35.4 + - - +
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Residues in contact with PHE 534 (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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507E ALA* 4.2 5.6 - - + -
509E ILE* 3.3 36.6 - - + -
510E SER* 3.4 44.4 - - - +
513E THR* 4.7 14.8 - - - +
515E LEU* 5.7 7.2 - - + -
530E THR 5.3 1.6 - - - -
531E ALA* 3.2 41.1 - - + -
533E SER* 1.3 78.1 - - - +
535E LEU* 1.3 68.4 + - + +
537E ASP* 4.5 4.0 - - - +
538E HIS* 2.9 33.5 + - - +
539E LEU 3.7 0.2 + - - -
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Residues in contact with LEU 535 (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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505E ILE* 5.8 5.2 - - + -
515E LEU* 6.3 1.8 - - + -
528E GLU* 4.6 17.7 - - + +
531E ALA* 3.3 31.4 - - + +
532E PHE* 3.3 35.4 - - + +
534E PHE* 1.3 89.8 - - + +
536E ARG* 1.3 63.9 + - - +
539E LEU* 3.2 48.9 - - + +
555E TRP* 4.9 10.3 - - + -
559E LEU* 3.3 22.9 - - + +
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Residues in contact with ARG 536 (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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692D HIS* 3.9 30.8 + - - -
715D ASN* 5.8 0.9 + - - -
532E PHE* 2.9 39.6 + - + +
533E SER* 3.0 20.7 + - - +
535E LEU* 1.3 79.9 - - - +
537E ASP* 1.3 71.0 + - - +
539E LEU 4.1 1.2 - - - +
559E LEU* 3.2 59.2 - - + +
560E LYS* 4.1 28.9 - - - +
561E ASN* 3.3 16.0 - - - +
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Residues in contact with ASP 537 (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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691D TRP* 5.4 0.3 + - - -
692D HIS* 3.4 34.8 + - - -
738D TYR* 3.0 21.7 + - - +
533E SER* 2.9 18.5 + - - +
534E PHE* 4.3 3.5 - - - +
536E ARG* 1.3 88.7 + - - +
538E HIS* 1.3 66.4 - - + +
539E LEU 3.5 3.3 + - - +
540E ARG* 4.0 4.2 + - - +
561E ASN* 2.8 23.3 + - - -
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Residues in contact with HIS 538 (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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513E THR* 3.0 37.8 + - + +
514E ASN* 3.9 12.2 - - - -
515E LEU 2.7 28.7 + - - +
516E GLN* 4.5 9.5 - - + +
534E PHE* 2.9 17.8 + - - +
537E ASP* 1.3 73.3 - - + +
539E LEU* 1.3 65.6 + - - +
540E ARG* 3.4 32.6 + - - +
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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