Contacts of the strand formed by residues 38 - 43 (chain O) in PDB entry 3MQT
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 TYR 38 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LYS* 3.6 21.1 - - + -
31O VAL 3.0 11.7 - - - +
32O THR* 3.6 16.8 - - + +
36O GLY 4.0 10.3 - - - -
37O VAL* 1.3 76.8 - - - +
39O GLY* 1.3 53.9 + - - +
40O LEU* 3.6 43.3 - - + +
112O LEU* 4.0 4.5 - - - -
115O LYS* 2.7 47.4 + - - +
373O LEU* 5.4 1.6 - - - +
375O ILE* 4.0 20.1 - - - +
386O PHE* 4.1 11.7 - + - -
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Residues in contact with GLY 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O VAL 3.6 0.5 - - - +
30O LYS* 3.5 0.9 - - - -
31O VAL 2.8 32.0 + - - -
38O TYR* 1.3 75.5 - - - +
40O LEU* 1.3 67.9 + - - +
108O ALA* 3.5 22.5 - - - +
111O ASP* 3.4 9.2 - - - -
112O LEU* 3.6 12.4 - - - +
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Residues in contact with LEU 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O ILE* 4.3 7.9 - - + -
29O VAL 3.3 6.3 - - - +
30O LYS* 3.8 15.3 - - + -
38O TYR* 3.6 32.1 - - + +
39O GLY* 1.3 83.3 - - - +
41O GLY* 1.3 60.6 + - - +
108O ALA* 3.5 11.2 - - - -
111O ASP* 2.9 16.0 + - - +
115O LYS* 5.8 0.4 - - - +
315O ILE* 4.4 4.7 - - + -
369O LEU* 3.7 19.9 - - - +
371O ILE* 3.9 25.4 - - + +
373O LEU* 3.9 39.0 - - + +
386O PHE* 3.9 11.0 - - + -
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Residues in contact with GLY 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ILE* 3.6 7.6 - - - +
29O VAL* 2.8 29.4 + - - +
40O LEU* 1.3 73.7 - - - +
42O GLU* 1.3 62.8 + - - +
104O GLY 3.5 18.2 - - - -
107O MET* 3.8 7.0 - - - -
108O ALA* 3.4 7.5 - - - +
315O ILE* 3.6 12.9 - - - +
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Residues in contact with GLU 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O THR* 2.6 29.5 + - - +
27O VAL 3.1 15.3 - - - +
29O VAL 4.3 0.9 - - - +
41O GLY* 1.3 74.6 - - - +
43O ALA* 1.3 60.7 + - - +
104O GLY* 3.3 13.2 - - - -
107O MET* 3.4 9.4 - - + +
284O ASN* 3.1 24.0 - - + +
312O LYS* 3.3 7.4 - - + +
313O THR* 3.0 40.5 + - - +
315O ILE* 3.8 11.3 - - + +
316O THR* 2.5 40.6 + - - +
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Residues in contact with ALA 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 4.3 20.9 - - + -
26O THR* 4.3 1.7 + - - -
27O VAL* 3.1 31.6 + - + +
29O VAL* 4.2 3.1 - - + +
42O GLU* 1.3 75.4 - - - +
44O ASP* 1.3 69.3 + - - +
50O MET* 4.7 2.0 - - + -
100O PHE 3.2 28.0 - - - +
101O ALA 4.3 0.2 - - - +
104O GLY* 4.0 7.6 - - - -
284O ASN* 3.9 4.0 - - - -
312O LYS* 4.1 6.9 + - - -
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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