Contacts of the helix formed by residues 537 - 541 (chain A) in PDB entry 3MDL
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 ASN 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A VAL* 2.8 41.2 + - - +
337A ILE* 3.9 5.0 - - - +
341A ILE* 4.0 13.7 - - + -
373A TYR* 4.0 1.6 - - - -
533A GLY 4.3 7.5 + - - +
534A LEU 3.5 16.5 + - - +
535A MET 3.1 1.7 - - - +
536A GLY* 1.3 79.4 - - - +
538A PRO* 1.3 76.7 - - - +
539A ILE* 3.1 36.2 + - - +
540A CYS* 3.0 21.5 + - - +
541A SER 3.9 1.9 + - - -
139B TRP* 3.7 12.0 - - - -
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Residues in contact with PRO 538 (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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373A TYR 5.4 2.0 - - - +
374A GLN* 6.3 0.4 - - - -
536A GLY 3.5 4.0 - - - +
537A ASN* 1.3 89.8 - - - +
539A ILE* 1.3 56.0 + - + +
540A CYS 3.1 0.2 - - - -
541A SER* 2.6 30.4 + - - +
544A TYR* 3.2 17.3 - - + +
127B PRO* 4.0 20.9 - - + -
139B TRP* 3.5 29.8 - - + -
142B PHE* 3.6 44.2 - - + -
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Residues in contact with ILE 539 (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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334A LEU* 4.2 30.5 - - + +
337A ILE* 4.0 11.0 - - + -
338A GLY* 3.5 36.1 - - - +
341A ILE* 4.3 4.9 - - + -
361A PHE* 5.0 2.2 - - + -
537A ASN* 3.1 22.4 + - - +
538A PRO* 1.3 76.6 - - - +
540A CYS* 1.3 67.5 + - - +
541A SER 3.3 0.2 - - - -
544A TYR* 3.6 18.2 - - + +
545A TRP* 3.3 39.5 + - + -
550A PHE* 4.3 22.2 - - + -
139B TRP* 4.6 5.8 - - + -
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Residues in contact with CYS 540 (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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341A ILE* 4.6 1.1 - - - -
361A PHE* 3.7 33.7 - - - -
363A PRO* 3.4 20.0 - - + +
367A PHE* 3.4 18.9 - - - -
373A TYR* 3.5 9.1 + - + -
534A LEU 3.6 23.3 - - - -
535A MET* 3.3 28.0 - - + +
537A ASN* 3.0 7.3 + - - +
539A ILE* 1.3 83.8 - - - +
541A SER* 1.3 62.6 + - - +
545A TRP* 4.4 0.7 - - - -
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Residues in contact with SER 541 (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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367A PHE* 4.1 0.2 - - - -
373A TYR* 3.7 18.7 - - - -
537A ASN 3.9 0.2 + - - -
538A PRO 2.6 21.2 + - - -
540A CYS* 1.3 79.0 - - - +
542A PRO* 1.3 69.7 - - - +
543A GLN* 4.2 3.5 + - - +
544A TYR* 3.0 19.8 + - - -
545A TRP* 2.8 26.2 + - - +
126B SER 5.1 0.4 - - - -
127B PRO* 3.7 28.2 - - - +
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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