Contacts of the strand formed by residues 36 - 45 (chain C) in PDB entry 5D4P
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLY* 3.2 5.4 - - - -
45A LYS* 2.8 63.7 + - + +
50A MET* 4.4 11.7 - - + +
201A ADP 3.4 9.9 - - - -
25C THR* 3.2 43.3 + - + +
28C LEU* 4.2 16.8 - - + -
29C ASP* 3.8 22.5 + - - -
33C VAL* 5.1 1.8 - - + -
35C GLY* 1.3 76.9 - - - +
37C THR* 1.3 64.6 + - - +
38C ILE* 3.8 24.7 - - + -
66C ILE* 4.2 11.0 - - + -
67C ILE 3.4 12.8 - - - +
68C ALA* 4.2 6.7 - - + -
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.5 17.0 - - + +
42A LEU* 4.0 27.8 - - + -
43A SER 3.6 10.8 - - - +
63A LEU* 4.6 2.2 - - + -
65A MET* 5.8 0.2 - - + -
201A ADP 2.8 41.1 + - - +
36C TYR* 1.3 71.3 - - - +
38C ILE* 1.3 68.9 + - - +
39C VAL 4.1 0.2 - - - -
65C MET 3.7 0.7 - - - +
66C ILE* 3.4 2.6 - - - -
67C ILE* 2.7 54.7 + - + +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.5 8.4 - - - +
43A SER* 2.8 52.4 + - - +
44A GLY 5.6 0.2 - - - +
50A MET* 6.5 0.2 - - + -
21C LYS* 3.4 36.1 - - + +
25C THR* 4.2 4.3 - - + -
36C TYR* 3.8 30.5 - - + -
37C THR* 1.3 78.6 - - - +
39C VAL* 1.3 65.2 + - - +
40C GLY* 3.9 2.4 + - - +
64C ILE* 4.0 29.4 - - + -
65C MET 3.4 7.4 - - - +
66C ILE* 4.1 9.9 - - + -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.3 4.5 - - + -
40A GLY 5.4 0.9 - - - +
41A ASN 5.2 0.9 - - - +
42A LEU* 3.6 26.0 - - + -
65A MET* 4.8 7.0 - - + -
39B VAL* 4.1 21.5 - - + -
37C THR* 5.1 0.4 - - + -
38C ILE* 1.3 73.4 - - - +
40C GLY* 1.3 64.3 + - - +
42C LEU* 3.9 20.3 - - + +
64C ILE* 3.4 4.2 - - - +
65C MET* 2.8 54.0 + - + +
67C ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.9 19.9 + - - +
39B VAL* 5.8 0.5 - - - +
38C ILE* 3.9 4.1 + - - +
39C VAL* 1.3 80.8 - - - +
41C ASN* 1.3 74.9 + - - +
42C LEU* 3.5 7.3 + - - +
58C ASN* 4.1 7.2 - - - -
63C LEU 4.1 0.2 - - - -
64C ILE* 4.1 14.1 - - - -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 4.0 7.9 - - - +
40B GLY* 4.5 14.8 + - - -
41B ASN* 5.9 4.9 - - - +
40C GLY* 1.3 75.7 - - - +
42C LEU* 1.3 63.9 + - - +
43C SER 4.3 0.2 + - - -
53C GLY* 3.5 4.5 - - - -
54C HIS* 2.7 51.5 + - - +
57C PHE 4.1 8.8 + - - +
58C ASN* 3.4 20.7 + - - +
59C GLU* 5.7 1.4 - - - +
62C ALA* 4.6 13.2 - - - +
63C LEU 3.6 6.0 + - - -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 3.6 20.2 - - + -
38B ILE 3.6 13.7 - - - +
39B VAL* 4.0 18.6 - - + -
15C ILE* 4.5 1.3 - - + -
39C VAL* 3.9 32.1 - - + +
40C GLY 3.9 4.5 - - - +
41C ASN* 1.3 77.7 - - - +
43C SER* 1.3 68.2 + - - +
51C TYR* 4.1 2.4 - - - +
52C GLU 4.2 0.9 - - - -
53C GLY* 3.4 14.7 + - - -
63C LEU* 3.1 35.6 + - + +
64C ILE* 3.5 30.1 - - - +
65C MET* 3.6 13.5 - - + +
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Residues in contact with SER 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 5.1 8.0 + - - -
37B THR* 3.4 10.2 - - - +
38B ILE* 2.8 47.9 + - - -
42C LEU* 1.3 75.6 - - - +
44C GLY* 1.3 59.7 + - - +
51C TYR 2.9 11.4 - - - -
52C GLU* 3.9 7.0 + - - -
53C GLY* 2.6 26.9 + - - -
63C LEU* 3.8 5.2 - - - +
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.1 20.6 - - - -
37B THR* 4.2 0.9 - - - -
38B ILE* 4.6 0.4 - - - +
43C SER* 1.3 77.8 - - - +
45C LYS* 1.3 61.1 + - - +
50C MET* 3.6 6.1 - - - +
51C TYR* 2.8 33.1 + - - +
63C LEU* 4.4 1.3 - - - -
201C ADP 3.4 16.0 + - - -
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 3.8 31.3 + - - +
33B VAL 5.5 2.2 + - - -
34B LYS 5.0 8.3 + - - -
35B GLY* 3.2 7.1 - - - -
36B TYR* 2.9 59.1 + - + +
44C GLY* 1.3 74.7 - - - -
46C GLY* 1.3 76.0 + - - +
47C SER* 5.6 0.4 - - - +
49C GLY 3.8 3.6 - - - +
50C MET* 3.4 30.5 - - + -
201C ADP 3.3 7.7 + - - -
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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