Contacts of the helix formed by residues 35 - 49 (chain F) in PDB entry 2P6T
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 SER 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F SER* 4.0 0.9 - - - -
34F LEU* 1.3 79.7 - - - +
36F PRO* 1.3 80.4 - - - +
37F SER* 3.3 2.6 + - - -
38F PRO* 3.1 27.4 - - - +
39F CYS* 3.0 20.1 + - - +
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Residues in contact with PRO 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ASN* 2.7 35.1 + - - +
26F VAL* 5.5 7.6 - - + -
29F SER* 4.0 15.0 - - - +
34F LEU 4.0 2.9 - - - +
35F SER* 1.3 89.7 - - - +
37F SER* 1.3 63.3 + - - +
39F CYS* 3.2 1.2 + - - +
40F LEU 3.1 10.6 + - - -
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Residues in contact with SER 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F SER* 3.7 0.9 + - - -
36F PRO* 1.3 81.2 - - - +
38F PRO* 1.3 66.9 - - - +
40F LEU* 3.1 8.5 + - - +
41F ARG* 3.0 28.2 + - - +
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Residues in contact with PRO 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 4.4 14.4 - - + -
35F SER* 3.1 32.5 - - - +
37F SER* 1.3 91.4 - - - +
39F CYS* 1.3 57.3 - - - +
41F ARG* 3.9 13.7 + - + +
42F ARG* 3.0 36.3 + - - +
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Residues in contact with CYS 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ILE* 4.4 7.4 - - - +
25F ASN* 3.5 8.5 - - - +
28F LEU* 3.6 34.3 - - - -
29F SER* 3.9 22.2 - - - -
32F VAL* 4.3 3.4 - - - -
34F LEU* 3.7 22.3 - - + +
35F SER 3.0 13.9 + - - +
36F PRO 3.3 9.6 - - - +
37F SER 3.1 0.2 - - - -
38F PRO* 1.3 75.7 - - - +
40F LEU* 1.3 58.6 + - - +
42F ARG* 2.9 21.8 + - - +
43F LEU* 3.0 12.4 + - - +
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ARG* 6.0 3.6 - - - +
25F ASN* 3.1 36.0 + - + +
36F PRO 3.1 1.4 + - - +
37F SER* 3.1 10.6 + - - +
39F CYS* 1.3 78.7 - - - +
41F ARG* 1.3 61.9 + - - +
43F LEU* 3.9 19.7 - - + -
44F LYS* 3.4 27.3 + - + +
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Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 5.4 4.0 - - - +
10F ASP* 5.6 0.2 + - - -
37F SER* 3.0 15.2 + - - +
38F PRO* 3.9 14.2 + - + +
39F CYS 3.1 0.2 - - - -
40F LEU* 1.3 77.1 - - - +
42F ARG* 1.3 98.9 + - - +
44F LYS* 3.4 6.5 + - - +
45F GLN* 3.2 59.4 + - + +
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASP* 2.8 41.2 + - - -
9F THR* 3.3 22.6 + - - +
10F ASP* 3.4 21.9 + - - +
13F ILE* 4.2 7.2 - - + -
34F LEU* 3.8 26.2 - - - +
38F PRO* 3.0 22.2 - - - +
39F CYS 2.9 6.5 + - - +
41F ARG* 1.3 108.6 - - - +
43F LEU* 1.3 64.5 + - - +
45F GLN* 3.5 6.5 + - - +
46F LEU* 3.1 28.5 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ARG* 5.0 11.4 - - - +
13F ILE* 4.6 5.3 - - + +
17F LEU* 3.3 35.4 - - + -
28F LEU* 3.4 20.2 - - + -
39F CYS 3.0 13.5 + - - +
40F LEU* 4.1 20.2 - - + +
41F ARG 3.3 0.2 - - - -
42F ARG* 1.3 76.0 - - - +
44F LYS* 1.3 60.0 + - - +
46F LEU* 3.3 12.6 + - + +
47F GLU* 2.9 41.3 + - + +
52F VAL* 5.9 2.5 - - + -
55F TYR* 3.0 26.5 - - + +
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Residues in contact with LYS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 3.4 18.7 + - + +
41F ARG* 3.7 9.2 - - - +
42F ARG 3.4 0.6 - - - -
43F LEU* 1.3 76.6 - - - +
45F GLN* 1.3 68.4 + - + +
47F GLU* 2.8 29.1 + - + +
48F ASP* 2.9 38.2 + - - +
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Residues in contact with GLN 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.7 37.1 - - + +
10F ASP* 5.1 3.8 + - - -
41F ARG* 3.2 48.4 + - + +
42F ARG* 3.5 11.2 + - - +
44F LYS* 1.3 80.0 - - + +
46F LEU* 1.3 65.5 + - + +
48F ASP* 3.3 6.9 + - - +
49F ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.5 18.2 - - + -
10F ASP* 4.0 27.1 - - + +
13F ILE* 4.1 18.4 - - + -
14F LEU* 4.0 17.7 - - + -
42F ARG 3.1 22.8 + - - +
43F LEU* 3.4 11.9 - - + +
44F LYS 3.1 0.4 - - - -
45F GLN* 1.3 80.2 - - + +
47F GLU* 1.3 61.8 + - - +
49F ALA* 3.6 3.9 + - - -
51F ILE* 3.1 59.5 + - + +
52F VAL* 3.5 13.4 + - + -
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 2.9 27.5 + - + +
44F LYS* 2.8 26.4 + - + +
46F LEU* 1.3 69.4 - - - +
48F ASP* 1.3 68.0 + - - +
50F GLY* 3.2 12.8 + - - -
52F VAL* 3.8 27.7 - - + +
55F TYR* 3.0 40.7 - - - +
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Residues in contact with ASP 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LYS* 2.9 40.2 + - - +
45F GLN* 3.9 5.5 + - - +
47F GLU* 1.3 73.0 - - - +
49F ALA* 1.3 55.3 + - - +
50F GLY* 2.6 18.4 + - - -
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Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E SER* 5.0 2.8 + - - -
4F LEU 5.9 5.2 - - - +
45F GLN 3.0 18.6 + - - +
46F LEU* 4.1 3.8 - - - +
48F ASP* 1.3 73.5 - - - +
50F GLY* 1.3 49.4 + - - -
51F ILE* 2.7 31.1 + - + +
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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