Contacts of the strand formed by residues 30 - 38 (chain I) in PDB entry 4MJI
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 30 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ALA 5.6 0.9 - - - +
25I TYR* 2.8 46.3 + - - +
27I THR* 3.5 26.1 - - - +
29I ILE* 1.3 87.4 - - - +
31I ASN* 1.3 66.1 + - - +
32I LEU 3.3 25.3 + - - +
33I GLN* 5.3 4.2 - - - +
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Residues in contact with ASN 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLU 4.6 0.2 - - - +
155F GLN* 2.6 67.4 + - - +
158F ALA* 3.4 27.8 - - - +
159F TYR* 4.2 11.6 - - + +
3H PHE* 5.0 2.8 - - - -
30I ASN* 1.3 75.5 - - - +
32I LEU* 1.3 71.8 + - + +
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Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F GLN* 3.3 39.0 - - - +
30I ASN* 3.2 19.4 + - - +
31I ASN* 1.3 86.2 - - + +
33I GLN* 1.3 62.0 + - - +
34I TRP* 3.2 53.6 - - + -
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Residues in contact with GLN 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I CYS* 3.8 26.8 - - - -
25I TYR* 3.8 30.7 - - + +
30I ASN* 5.3 4.0 - - - +
32I LEU* 1.3 76.9 - - - +
34I TRP* 1.3 104.2 + - - +
35I TYR* 4.8 10.3 - - + -
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Residues in contact with TRP 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU* 3.2 41.3 - - + -
33I GLN* 1.3 100.6 + - - +
35I TYR* 1.3 70.4 + - - +
36I ARG* 2.6 52.5 + - - +
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Residues in contact with TYR 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I MET* 3.5 35.9 + - + -
22I ASN* 3.7 2.1 - - - -
23I CYS* 3.4 39.3 + - + +
33I GLN* 4.8 13.9 - - + -
34I TRP* 1.3 84.6 - - - +
36I ARG* 1.3 74.3 + - - +
37I GLN 4.3 0.5 + - - -
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Residues in contact with ARG 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I TRP* 2.6 53.8 + - - +
35I TYR* 1.3 86.0 + - - +
37I GLN* 1.3 61.4 + - - +
38I ASN* 4.0 1.6 + - - +
44I VAL* 3.8 37.0 - - + +
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Residues in contact with GLN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I TYR 4.3 0.6 + - - -
36I ARG* 1.3 73.2 - - - +
38I ASN* 1.3 63.5 + - - +
39I SER* 5.1 6.0 - - - -
43I LEU* 3.6 23.7 - - + +
44I VAL* 3.0 27.4 - - - -
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Residues in contact with ASN 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ARG 4.0 2.5 + - - +
37I GLN* 1.3 75.6 - - - +
39I SER* 1.3 69.9 + - - +
40I GLY 4.8 2.3 - - - +
41I ARG 4.6 2.9 - - - +
42I GLY 4.3 1.7 - - - +
43I LEU* 2.5 28.9 + - - +
44I VAL* 3.6 14.6 - - + +
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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