Contacts of the strand formed by residues 42 - 46 (chain A) in PDB entry 1MDF
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 ILE 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.4 7.5 + - - +
41A ARG* 1.3 77.3 - - - +
43A ALA* 1.3 61.9 + - - +
44A ILE 3.7 14.4 - - - +
45A THR* 3.5 25.1 - - - +
50A HIS* 3.4 33.7 - - + +
51A TRP 4.1 0.7 - - - +
52A SER* 4.3 12.8 - - - +
53A TYR* 4.0 2.2 - - - -
251A GLY 3.8 8.8 - - - +
252A ARG* 3.6 28.1 - - + +
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Residues in contact with ALA 43 (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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41A ARG 3.3 1.0 + - - -
42A ILE* 1.3 74.8 - - - +
44A ILE* 1.3 70.8 + - + +
51A TRP 2.9 13.6 + - - +
52A SER 4.5 0.2 - - - +
53A TYR* 3.3 49.4 - - + +
56A LEU* 5.0 4.5 - - + -
247A LEU* 4.1 10.6 - - + +
252A ARG* 3.9 1.4 - - - -
253A VAL* 3.0 29.1 + - - +
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Residues in contact with ILE 44 (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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42A ILE* 3.7 3.4 - - - +
43A ALA* 1.3 89.5 - - + +
45A THR* 1.3 65.4 + - - +
50A HIS* 3.5 4.5 - - - -
51A TRP* 3.1 50.6 + - + +
56A LEU* 4.1 15.7 - - + -
86A LYS* 4.1 16.3 - - + +
89A PHE* 3.4 48.9 - - + -
247A LEU* 4.7 5.2 - - + -
253A VAL* 3.5 7.2 - - + +
255A LEU* 3.8 30.7 - - + -
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Residues in contact with THR 45 (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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42A ILE* 3.5 11.8 - - - +
44A ILE* 1.3 73.2 - - - +
46A CYS* 1.3 64.6 + - - +
47A GLY 4.1 13.5 - - - +
49A THR 3.7 4.9 - - - +
50A HIS* 3.6 15.7 + - + +
252A ARG* 3.1 39.6 + - - +
253A VAL 2.6 15.4 + - - +
254A VAL* 4.3 7.7 - - + +
255A LEU* 2.8 29.8 + - - +
271A GLU* 4.1 15.7 - - + -
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Residues in contact with CYS 46 (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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44A ILE 4.3 0.4 - - - -
45A THR* 1.3 74.5 - - - +
47A GLY* 1.3 68.9 + - - +
48A ASN 3.2 0.2 + - - -
49A THR* 2.4 39.4 + - - +
84A ASN 4.5 7.2 - - - -
85A ILE* 4.7 9.4 - - - -
86A LYS* 3.7 30.7 - - + +
255A LEU* 4.0 26.9 - - + -
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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