Contacts of the helix formed by residues 36 - 50 (chain C) in PDB entry 2Y4T
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 ASP 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C MET* 3.1 32.3 - - - +
35C ALA* 1.3 79.3 - - - +
37C VAL* 1.3 85.3 + - + +
39C LYS* 4.3 6.8 + - - +
40C HIS* 3.2 23.5 + - - -
66C GLY* 5.6 4.9 - - - -
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Residues in contact with VAL 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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34C MET* 3.0 13.4 + - + +
36C ASP* 1.3 91.5 + - - +
38C GLU* 1.3 65.8 + - - +
39C LYS 3.2 2.5 - - - -
40C HIS* 2.9 26.0 + - - +
41C LEU* 3.4 19.6 + - + +
63C ALA* 3.3 30.5 - - - +
66C GLY* 3.4 37.7 - - - +
67C ASP* 3.7 11.0 - - + +
70C ASN* 4.1 9.2 - - - +
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C MET 2.6 35.7 + - - +
37C VAL* 1.3 73.3 - - - +
39C LYS* 1.3 67.6 + - + +
41C LEU* 3.1 26.6 + - - +
42C GLU* 3.0 40.8 + - - +
72C ILE* 6.0 2.3 - - - +
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Residues in contact with LYS 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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50B ALA* 5.1 17.0 - - + -
35C ALA* 3.3 33.2 - - - +
36C ASP 4.3 8.5 - - - +
37C VAL 3.1 0.8 + - - -
38C GLU* 1.3 83.0 - - - +
40C HIS* 1.3 64.5 + - + +
42C GLU* 3.3 27.4 + - - +
43C LEU* 3.2 30.5 + - + +
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Residues in contact with HIS 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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50B ALA* 6.5 0.2 - - + -
52B GLN* 3.0 38.1 + - + -
36C ASP* 3.2 24.9 + - + -
37C VAL* 2.9 12.9 + - - +
39C LYS* 1.3 79.8 - - + +
41C LEU* 1.3 51.9 + - - +
43C LEU* 3.3 1.8 + - + +
44C GLY* 2.8 31.4 + - - -
59C GLN* 3.3 42.5 - - - +
62C ALA* 3.5 31.8 + - + +
63C ALA* 4.1 4.9 - - + +
66C GLY* 6.3 0.6 - - - -
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Residues in contact with LEU 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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34C MET 5.9 0.4 - - - +
37C VAL* 3.4 15.9 + - + +
38C GLU* 3.1 33.3 + - - +
40C HIS* 1.3 77.4 - - - +
42C GLU* 1.3 58.0 + - - +
45C LYS* 3.0 31.4 + - - +
60C PHE* 3.8 17.0 - - + -
63C ALA* 3.8 13.2 - - + -
70C ASN* 3.5 21.3 - - - +
72C ILE* 4.2 17.9 - - + -
73C ALA* 3.8 30.7 - - - +
76C ARG* 4.3 8.8 + - + +
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Residues in contact with GLU 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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38C GLU* 3.0 28.1 + - - +
39C LYS* 3.3 51.3 + - - +
41C LEU* 1.3 76.3 - - - +
43C LEU* 1.3 61.9 + - + +
45C LYS* 3.7 9.0 - - - +
46C LYS* 3.4 24.1 + - - +
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Residues in contact with LEU 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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43B LEU* 4.7 6.0 - - + +
46B LYS* 3.7 33.2 - - + -
47B LEU* 3.9 24.5 - - + +
50B ALA* 3.6 29.8 - - + -
52B GLN* 4.6 0.9 - - + -
39C LYS* 3.2 22.6 + - + +
40C HIS* 5.6 0.7 - - + -
42C GLU* 1.3 78.1 - - + +
44C GLY* 1.3 59.6 + - - +
46C LYS* 3.1 10.9 + - + +
47C LEU* 3.0 34.0 + - + +
59C GLN* 3.4 25.8 - - + +
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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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40C HIS 2.8 20.7 + - - -
43C LEU* 1.3 72.4 - - - +
45C LYS* 1.3 52.5 + - - +
47C LEU* 3.4 0.8 + - - -
48C LEU* 2.8 35.7 + - - +
56C ALA* 3.5 10.5 - - - +
59C GLN* 3.7 16.5 - - - +
60C PHE* 3.2 20.6 - - - -
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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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41C LEU 3.0 19.5 + - - +
42C GLU* 3.7 9.4 - - - +
44C GLY* 1.3 74.8 - - - +
46C LYS* 1.3 53.5 + - - +
48C LEU* 3.3 6.2 + - + +
49C ALA* 2.8 39.2 + - + +
60C PHE* 3.4 9.7 - - + -
76C ARG* 3.6 40.3 - - - +
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Residues in contact with LYS 46 (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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43B LEU* 3.7 21.8 - - + -
46B LYS* 3.8 31.7 - - + +
42C GLU 3.4 11.5 + - - +
43C LEU* 3.1 14.4 + - + +
45C LYS* 1.3 80.0 - - + +
47C LEU* 1.3 57.0 + - - +
49C ALA* 3.4 6.6 + - - +
50C ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 47 (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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43B LEU* 3.8 24.9 - - + -
47B LEU* 3.8 20.0 - - + -
59B GLN* 3.6 34.8 - - + +
43C LEU* 3.0 17.0 + - + +
44C GLY 3.7 5.6 - - - +
46C LYS* 1.3 74.1 - - - +
48C LEU* 1.3 59.6 + - - +
50C ALA* 3.1 7.8 + - - +
52C GLN* 2.7 49.5 + - + +
55C ASP* 3.8 30.5 - - + +
56C ALA* 4.0 3.4 - - - +
59C GLN* 4.3 11.9 - - + -
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Residues in contact with LEU 48 (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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44C GLY 2.8 20.2 + - - +
45C LYS* 3.5 6.5 - - + +
47C LEU* 1.3 70.6 - - - +
49C ALA* 1.3 56.7 + - - +
51C GLY* 2.8 24.9 + - - -
52C GLN 4.6 3.6 - - - +
53C LEU* 4.7 14.6 - - + +
56C ALA* 3.7 7.2 - - + +
60C PHE* 3.7 13.5 - - + -
76C ARG* 4.3 5.4 - - - +
79C THR* 3.9 17.5 - - - +
80C VAL* 3.6 35.9 - - + +
83C ALA* 5.5 5.4 - - + -
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Residues in contact with ALA 49 (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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45C LYS* 2.8 24.0 + - + +
46C LYS* 3.5 9.2 - - + +
48C LEU* 1.3 73.4 - - - +
50C ALA* 1.3 57.7 + - - +
51C GLY 3.3 2.9 + - - -
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Residues in contact with ALA 50 (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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39B LYS* 5.1 13.7 - - + -
40B HIS* 5.7 0.7 - - + -
43B LEU* 3.9 26.2 - - + -
46C LYS 2.8 16.6 + - - +
47C LEU 3.1 5.1 + - - +
49C ALA* 1.3 75.1 - - - +
51C GLY* 1.3 58.8 + - - +
52C GLN* 3.2 16.8 + - + +
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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