Contacts of the strand formed by residues 54 - 57 (chain A) in PDB entry 1M8U
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 GLN 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 3.7 8.8 - - + +
44A ILE 3.3 4.3 - - - +
45A TYR* 3.5 30.8 + - + -
52A GLY 4.4 6.2 + - - +
53A PRO* 1.3 73.8 - - + +
55A TYR* 1.3 76.2 + - - +
143A GLN* 3.0 44.5 + - - +
144A TYR* 3.8 14.3 - - - +
145A LEU* 2.9 35.3 + - - +
157A TRP 4.8 4.8 + - - -
158A GLY* 5.8 2.6 + - - -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 3.2 9.0 - - - +
44A ILE* 2.8 57.2 + - + -
46A GLU* 5.1 4.9 + - + -
53A PRO* 3.5 32.9 - - + +
54A GLN* 1.3 84.2 - - - +
56A PHE* 1.3 58.2 + - - +
57A LEU* 3.2 7.7 - - + +
68A TRP* 3.5 40.8 - + + +
69A MET 3.3 20.0 - - - -
70A GLY* 3.5 10.5 - - - -
71A LEU* 3.4 31.0 + - + +
75A ILE* 4.5 10.8 - - + -
142A ARG* 6.5 1.6 - - - -
143A GLN* 3.7 11.7 - - + -
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Residues in contact with PHE 56 (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 CYS* 3.9 22.0 - - + -
42A TRP 3.4 8.7 - - - -
43A MET* 3.7 8.0 - - - +
55A TYR* 1.3 69.9 - - - +
57A LEU* 1.3 77.8 + - - +
58A ARG* 3.3 47.8 - - + -
62A TYR* 4.3 3.7 + - - -
68A TRP* 4.6 7.1 - - - +
69A MET* 6.0 1.7 - - - +
81A ILE* 3.8 21.1 - - + -
132A VAL* 3.7 19.5 - - + -
134A TYR* 3.7 18.6 - - - +
143A GLN* 2.8 22.8 + - - +
168A ARG* 3.8 17.5 - - - -
170A ALA* 4.0 15.7 - - + -
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Residues in contact with LEU 57 (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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3A ILE* 5.1 1.6 - - + -
35A ILE* 5.0 5.8 - - + -
37A VAL* 4.1 18.4 - - + -
40A GLY 4.3 0.5 - - - +
41A CYS* 3.6 4.9 - - - -
42A TRP* 2.8 41.6 + - + +
44A ILE* 3.5 33.2 - - + -
55A TYR* 3.2 19.5 - - + +
56A PHE* 1.3 85.4 - - - +
58A ARG* 1.3 61.7 + - - +
62A TYR* 3.3 40.4 - - + -
68A TRP* 3.3 22.2 - - + -
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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