Contacts of the helix formed by residues 41 - 52 (chain C) in PDB entry 2P82
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 GLU 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLN 4.4 1.7 - - - +
36C HIS* 3.6 9.4 - - - +
37C LEU* 2.9 55.9 + - + +
40C THR* 1.3 88.5 - - + +
42C LYS* 1.3 65.1 + - - +
43C SER* 3.4 2.5 - - - -
44C LYS* 3.3 37.3 + - + +
45C LEU* 3.0 20.8 + - - +
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Residues in contact with LYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU 3.7 0.8 + - - -
38C LEU* 3.5 37.0 + - - +
39C LYS* 3.5 15.7 + - - +
40C THR 3.6 0.8 + - - -
41C GLU* 1.3 74.6 - - - +
43C SER* 1.3 57.5 + - - +
45C LEU* 3.1 10.1 + - + +
46C LEU* 2.9 55.8 + - + +
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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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41C GLU* 3.4 0.5 - - - -
42C LYS* 1.3 77.4 - - - +
44C LYS* 1.3 60.6 + - - +
46C LEU* 4.1 8.1 - - - +
47C SER* 3.0 32.6 + - - -
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Residues in contact with LYS 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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34C LYS* 4.9 11.1 - - - +
35C GLN 4.5 6.2 + - - -
36C HIS* 3.8 22.5 + - + +
41C GLU* 3.3 46.6 + - + +
42C LYS 3.2 0.6 - - - -
43C SER* 1.3 82.3 + - - +
45C LEU* 1.3 58.2 + - - +
47C SER* 4.0 5.3 + - - -
48C ASP* 3.0 29.3 + - - +
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Residues in contact with LEU 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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29C VAL* 3.8 22.7 - - + -
31C ILE* 3.7 29.2 - - + -
36C HIS* 3.7 24.8 + - + -
37C LEU 5.2 0.2 - - - +
38C LEU* 4.1 33.2 - - + +
41C GLU 3.0 12.8 + - - +
42C LYS* 3.1 10.7 + - + +
44C LYS* 1.3 74.9 - - - +
46C LEU* 1.3 74.2 + - + +
48C ASP* 3.3 3.3 + - - +
49C ILE* 3.1 37.8 + - + +
276C ILE* 5.4 1.3 - - + -
306C PRO* 5.6 2.5 - - + -
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Residues in contact with LEU 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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42C LYS* 2.9 46.0 + - + +
43C SER* 4.1 6.7 - - - +
45C LEU* 1.3 82.8 - - + +
47C SER* 1.3 57.5 + - - +
49C ILE* 3.4 5.7 + - - +
50C SER* 3.0 33.1 + - - +
305C SER* 5.4 1.6 - - - -
306C PRO* 3.5 37.9 - - + -
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Residues in contact with SER 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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43C SER 3.0 19.4 + - - -
44C LYS* 4.0 4.7 + - - -
46C LEU* 1.3 75.6 - - - +
48C ASP* 1.3 59.8 + - - +
50C SER* 3.9 5.6 - - - -
51C ALA* 2.9 31.2 + - - +
100C SER* 3.7 15.2 + - - -
101C TRP* 5.7 0.7 - - - -
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Residues in contact with ASP 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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31C ILE* 3.9 6.5 - - - +
34C LYS* 3.5 5.3 - - - +
36C HIS* 2.8 29.8 + - + +
44C LYS 3.0 19.8 + - - +
45C LEU 3.5 4.7 - - - +
47C SER* 1.3 78.2 + - - +
49C ILE* 1.3 60.8 + - + +
51C ALA* 3.5 6.2 + - - -
52C ARG* 2.9 54.4 + - - -
97C ARG* 2.8 33.7 + - - -
99C TRP 5.4 0.7 - - - +
100C SER* 5.5 1.3 - - - -
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Residues in contact with ILE 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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31C ILE* 4.0 26.5 - - + -
45C LEU* 3.1 32.7 + - + +
46C LEU* 3.8 6.7 - - - +
47C SER 3.3 0.2 - - - -
48C ASP* 1.3 76.6 - - - +
50C SER* 1.3 62.9 + - - +
52C ARG* 3.3 25.4 + - - +
268C ILE* 4.1 17.0 - - + -
276C ILE* 4.2 7.6 - - + -
277C PHE 6.0 0.2 - - - +
278C LEU* 4.1 19.0 - - + +
302C CYS* 4.7 5.0 + - + +
304C GLN 5.8 2.9 - - - +
306C PRO* 3.6 42.2 - - + -
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Residues in contact with SER 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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46C LEU* 3.0 20.0 + - - +
47C SER* 4.0 7.0 - - - -
49C ILE* 1.3 76.7 - - - +
51C ALA* 1.3 51.0 + - - +
52C ARG 3.3 3.0 + - - +
101C TRP* 3.9 9.1 - - - -
301C HIS* 2.8 38.3 + - - +
302C CYS 2.8 26.7 + - - +
303C LEU* 3.9 20.9 + - - +
304C GLN 5.5 0.5 + - - -
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Residues in contact with ALA 51 (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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47C SER 2.9 19.4 + - - +
48C ASP* 3.5 9.2 - - - +
49C ILE 3.2 0.2 - - - -
50C SER* 1.3 74.7 - - - +
52C ARG* 1.3 76.7 + - - +
53C LEU 3.5 0.7 + - - -
99C TRP* 3.3 18.3 - - + -
100C SER* 4.0 7.2 - - - +
101C TRP* 3.9 34.5 - - + +
301C HIS* 3.1 15.2 - - - -
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Residues in contact with ARG 52 (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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31C ILE* 5.1 2.9 - - - -
32C LEU* 4.0 22.6 - - + +
48C ASP* 2.9 46.3 + - - -
49C ILE* 3.3 15.9 - - - +
50C SER 3.3 4.9 - - - +
51C ALA* 1.3 93.3 - - - +
53C LEU* 1.3 64.3 + - - +
54C TRP* 3.3 4.9 + - - +
88C GLN* 2.9 37.8 + - + +
91C ILE* 4.0 19.6 - - - +
92C CYS* 5.4 0.6 - - - -
97C ARG* 3.5 16.9 + - - +
99C TRP* 4.2 15.4 + - - -
266C TYR* 5.4 3.1 - - + -
268C ILE* 4.8 5.8 - - + -
278C LEU* 3.7 23.7 - - + +
300C PHE 3.8 0.9 - - - +
301C HIS* 3.4 11.8 + - - -
302C CYS 4.7 0.5 + - - -
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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