Contacts of the strand formed by residues 439 - 443 (chain A) in PDB entry 3MHS
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 TRP 439 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A THR* 5.8 2.2 - - + -
413A LEU* 3.8 40.6 - - + -
414A ILE 3.9 8.5 - - - -
415A GLY* 4.1 1.6 - - - -
416A ILE* 4.6 2.7 - - + -
431A PHE* 3.7 18.8 - - + -
432A CYS 3.3 25.1 - - - -
433A LYS* 3.5 38.0 - - + +
437A GLY 3.6 13.5 - - - -
438A GLN* 1.3 95.4 + - - +
440A PHE* 1.3 62.1 + - - +
449A SER* 3.8 0.2 - - - -
450A ILE* 3.2 26.2 + - + +
452A GLN* 3.1 47.0 - - + +
455A VAL* 3.7 37.7 - - + -
456A LEU* 5.9 1.3 - - + -
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Residues in contact with PHE 440 (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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136A LEU* 3.8 27.1 - - + -
431A PHE* 3.2 5.9 - - - +
432A CYS 2.9 33.9 + - - -
434A ILE* 3.6 29.8 - - + -
438A GLN* 3.0 36.1 - - + -
439A TRP* 1.3 76.1 - - - +
441A LYS* 1.3 60.3 + - - +
442A PHE* 3.5 23.1 - + + -
447A VAL* 4.3 5.2 - - + -
448A SER 3.1 15.7 - - - +
449A SER* 3.7 14.8 - - - -
450A ILE* 4.0 4.0 - - - -
48C TYR* 3.6 25.6 - + - -
58C ILE* 3.8 18.6 - - + -
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Residues in contact with LYS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.7 34.7 - - + +
430A ALA 3.5 3.6 - - - -
431A PHE* 3.5 30.7 - - + -
440A PHE* 1.3 72.1 - - - +
442A PHE* 1.3 64.3 + - - +
443A ASN* 3.9 12.4 - - + +
446A MET 3.4 2.3 - - - +
447A VAL* 3.3 5.7 - - - +
448A SER* 2.8 48.0 + - - +
450A ILE* 4.0 15.2 - - + +
458A GLU* 5.4 3.0 + - - -
54C GLY 5.7 3.2 + - - -
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Residues in contact with PHE 442 (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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136A LEU* 3.6 16.8 - - + -
137A SER 4.5 2.9 - - - -
150A SER* 5.5 2.4 - - - -
153A GLN* 3.3 48.7 - - + +
157A HIS* 3.5 22.9 - + - -
428A TYR 4.9 0.2 - - - +
429A ILE* 3.4 5.9 - - - +
430A ALA* 2.7 39.1 + - + +
432A CYS* 3.6 31.9 - - + -
434A ILE* 6.1 0.4 - - + -
440A PHE* 3.5 28.9 - + + -
441A LYS* 1.3 70.5 - - - +
443A ASN* 1.3 60.3 + - - +
444A ASP 3.7 5.6 + - - +
446A MET 3.7 3.4 - - - -
447A VAL* 3.8 30.1 - - + -
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Residues in contact with ASN 443 (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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427A HIS* 2.7 31.5 + - - -
429A ILE* 3.6 30.5 - - + +
441A LYS* 4.7 12.6 - - + +
442A PHE* 1.3 72.1 - - - +
444A ASP* 1.3 67.9 + - - +
445A SER 3.0 1.4 + - - -
446A MET* 2.9 34.7 + - + +
63C LYS* 5.9 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