Contacts of the strand formed by residues 32 - 36 (chain M) in PDB entry 5XTD
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 32 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ASN 4.5 5.8 - - - +
31M LEU* 1.3 74.6 - - - +
33M GLU* 1.3 64.8 + - - +
34M VAL* 4.1 4.3 - - + -
41M VAL 3.4 0.2 - - - +
42M MET* 3.5 0.7 - - - -
43M VAL* 2.8 40.7 + - + +
44M GLU 4.8 1.3 - - - +
45M PRO* 3.5 35.0 - - + -
46M GLY 4.8 1.6 - - - +
96M VAL* 5.3 4.0 - - + +
97M MET* 4.0 8.3 - - - -
98M LYS* 3.3 40.2 - - + +
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Residues in contact with GLU 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M LEU 3.7 1.4 + - - +
32M ILE* 1.3 72.1 - - - +
34M VAL* 1.3 69.4 + - - +
35M PHE* 3.1 46.9 - - - -
40M SER* 2.9 29.5 + - - +
41M VAL 3.2 7.6 - - - +
42M MET* 4.7 12.1 - - - +
98M LYS* 3.1 56.5 + - - +
99M GLY* 3.7 2.6 + - - -
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Residues in contact with VAL 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ILE* 3.9 2.2 + - + -
33M GLU* 1.3 84.5 - - - +
35M PHE* 1.3 67.0 + - - +
36M VAL 3.6 0.2 + - - -
41M VAL* 2.9 36.5 + - - +
43M VAL* 3.6 23.1 - - + -
52M ALA* 6.0 2.5 - - + -
96M VAL* 4.0 9.4 - - + -
97M MET 3.1 35.0 - - - +
99M GLY 4.9 0.7 - - - +
100M TRP* 3.2 34.3 - - + +
101M ASN* 4.9 0.4 - - - -
102M ILE* 5.3 10.5 - - + -
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Residues in contact with PHE 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M GLU* 3.1 36.6 - - - -
34M VAL* 1.3 71.3 - - - +
36M VAL* 1.3 59.4 + - - +
38M GLY 3.7 12.8 - - - +
39M GLN 3.3 6.5 - - - +
40M SER* 3.5 24.2 - - - -
99M GLY* 5.0 9.9 - - - -
100M TRP 3.0 18.7 + - - +
101M ASN* 2.9 41.8 - - + +
102M ILE* 3.0 18.9 + - - +
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Residues in contact with VAL 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M VAL 3.6 3.0 + - - +
35M PHE* 1.3 72.5 - - - +
37M ASP* 1.3 74.3 + - + +
38M GLY 2.3 22.3 + - - -
39M GLN* 2.8 29.0 + - + +
41M VAL* 3.5 21.3 - - + +
52M ALA* 4.0 15.5 - - + +
53M CYS* 4.5 3.1 - - - -
56M VAL* 3.7 35.7 - - + -
58M MET* 5.3 5.2 - - + -
102M ILE* 3.5 21.5 - - + +
104M THR* 5.8 3.4 - - + +
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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