Contacts of the strand formed by residues 44 - 48 (chain Y) in PDB entry 1MHP
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 LYS 44 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35Y TYR* 3.2 6.0 - - - -
36Y GLN* 2.9 66.1 + - - +
38Y LYS* 4.1 2.1 - - - +
41Y LYS* 3.3 30.3 - - - +
42Y ALA 4.5 4.3 + - - +
43Y PRO* 1.3 77.7 - - - +
45Y PRO* 1.3 77.6 - - + +
46Y TRP* 3.2 14.8 + - + +
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Residues in contact with PRO 45 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104X TYR* 3.5 26.5 - - + +
105X PHE 3.6 9.0 - - - +
106X ASP* 2.6 30.3 - - - +
107X VAL* 5.6 0.4 - - - -
108X TRP* 4.0 11.0 - - + +
35Y TYR* 3.7 12.5 - - + -
43Y PRO 4.4 0.2 - - - +
44Y LYS* 1.3 90.0 - - + +
46Y TRP* 1.3 67.4 + - - +
54Y ALA* 3.2 18.7 - - + +
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Residues in contact with TRP 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X TYR* 5.2 0.4 + - - -
34Y TRP* 2.8 25.0 + - + +
35Y TYR* 4.2 0.9 - - - -
36Y GLN* 2.9 54.1 - - + +
44Y LYS* 3.2 19.0 + - + +
45Y PRO* 1.3 84.0 - - - +
47Y ILE* 1.3 75.7 + - + +
53Y LEU* 3.8 0.7 - - - -
54Y ALA* 2.9 24.4 + - - -
56Y GLY* 5.3 1.6 - - - -
57Y VAL* 3.0 53.7 - - + +
58Y PRO* 4.1 7.2 - - + -
61Y PHE* 3.4 42.8 - + - -
72Y LEU* 4.5 2.0 - - + -
81Y ASP* 5.5 0.7 - - - -
85Y TYR* 3.9 12.7 - + - -
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Residues in contact with ILE 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X TYR* 5.0 1.7 - - - -
33Y PHE* 3.2 6.1 - - - +
34Y TRP* 2.7 48.5 + - + +
46Y TRP* 1.3 97.3 - - + +
48Y TYR* 1.3 58.5 + - - +
50Y THR 3.1 31.4 - - - +
51Y SER* 3.8 6.7 - - - -
52Y ASN 3.2 13.7 - - - +
53Y LEU* 4.0 13.7 - - + -
61Y PHE* 4.9 0.7 - - + -
62Y SER 3.8 3.1 - - - +
63Y GLY* 3.8 18.2 - - - +
72Y LEU* 3.3 35.7 - - + -
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Residues in contact with TYR 48 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU* 3.2 40.3 - - + +
104X TYR* 3.2 46.0 - + + -
33Y PHE* 3.4 9.6 - - + -
47Y ILE* 1.3 73.4 - - - +
49Y LEU* 1.3 97.5 + - + +
50Y THR 3.0 4.4 + - - -
51Y SER 3.7 0.2 + - - -
52Y ASN* 2.8 55.0 + - + +
53Y LEU 3.4 28.1 + - - -
54Y ALA* 4.1 7.4 - - - -
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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