Contacts of the helix formed by residues 40 - 51 (chain F) in PDB entry 5L08
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 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E ARG* 2.8 39.6 + - - +
119E SER* 5.6 1.2 + - - -
122E PHE* 5.6 0.9 - - - -
8F TYR* 6.2 1.3 - - - -
11F GLY 6.0 0.4 - - - +
12F GLU* 5.9 4.3 - - - +
19F LEU* 3.7 12.8 - - - +
38F ILE* 3.4 8.0 - - - +
39F LYS* 1.3 78.2 - - - +
41F ALA* 1.3 63.4 + - - +
42F LEU* 3.1 9.8 + - - +
43F MET* 2.8 28.7 + - - +
44F LEU 3.2 14.2 + - - -
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Residues in contact with ALA 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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11F GLY* 3.4 37.7 + - - +
14F LEU* 3.5 29.2 - - + +
19F LEU* 4.3 3.6 - - - -
40F ASP* 1.3 76.2 - - - +
42F LEU* 1.3 58.7 + - - +
44F LEU* 2.9 5.7 + - - +
45F PHE* 2.8 45.4 + - + -
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Residues in contact with LEU 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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119E SER* 5.1 2.9 - - - +
122E PHE* 3.3 37.2 - - + -
123E LEU* 4.5 2.0 - - - +
126E GLU* 3.1 29.4 - - + +
4F SER* 4.8 1.8 - - - +
7F LEU* 5.3 1.3 - - + -
8F TYR* 3.6 40.2 - - + +
11F GLY* 5.3 0.8 - - - -
40F ASP* 3.1 7.6 + - - +
41F ALA* 1.3 77.6 - - - +
43F MET* 1.3 57.6 + - - +
45F PHE* 3.0 26.7 + - + +
46F GLN* 2.8 38.9 + - - +
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Residues in contact with MET 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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118E ARG* 4.1 14.4 - - - +
121E LYS* 4.5 5.2 - - - +
122E PHE* 2.3 52.9 - - + -
37F PRO* 3.9 23.6 - - + +
38F ILE* 3.4 32.5 - - + +
39F LYS* 4.2 3.4 - - + +
40F ASP* 2.8 36.4 + - - +
42F LEU* 1.3 77.1 - - - +
44F LEU* 1.3 61.5 + - - +
46F GLN* 3.2 12.7 + - - +
47F ARG* 3.2 16.2 + - - +
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 3.8 19.3 - - + -
22F LEU* 3.8 33.7 - - + +
23F LYS* 4.6 11.7 - - + +
26F SER* 4.6 15.9 - - - +
30F ILE* 5.0 6.1 - - + -
35F GLN* 5.1 3.6 - - + -
38F ILE* 3.3 24.3 - - + +
40F ASP 3.2 4.7 + - - +
41F ALA* 2.9 10.4 + - - +
43F MET* 1.3 78.2 - - - +
45F PHE* 1.3 65.7 + - + +
47F ARG* 2.9 15.9 + - + +
48F LEU* 2.8 45.0 + - + +
65F LEU* 5.7 2.9 - - + -
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Residues in contact with PHE 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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7F LEU* 3.4 43.7 - - + -
10F ILE* 5.5 2.9 - - + -
11F GLY* 5.0 2.9 - - - -
14F LEU* 5.8 0.7 - - + -
22F LEU* 5.4 4.9 - - + -
41F ALA* 2.8 37.6 + - + -
42F LEU* 3.0 24.9 + - + +
44F LEU* 1.3 85.7 - - + +
46F GLN* 1.3 54.2 + - - +
48F LEU* 3.1 17.0 + - + +
49F GLN* 2.7 34.4 + - - +
54F LEU* 3.6 22.4 - - + +
62F LEU* 3.8 37.0 - - + -
65F LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 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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122E PHE* 2.8 54.9 + - + +
125E GLN* 2.7 36.9 + - - +
126E GLU* 4.9 5.5 - - - +
42F LEU* 2.8 26.7 + - - +
43F MET 3.3 8.5 - - - +
44F LEU 3.1 0.2 - - - -
45F PHE* 1.3 77.8 - - - +
47F ARG* 1.3 78.9 + - - +
49F GLN* 3.3 11.9 + - - +
50F GLU* 2.8 22.3 + - - +
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Residues in contact with ARG 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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122E PHE* 5.1 3.2 - - - -
30F ILE* 3.7 21.5 - - + +
34F LYS* 3.7 30.9 - - + +
35F GLN* 5.2 1.1 - - - -
37F PRO* 5.8 2.9 - - - +
38F ILE* 3.5 32.4 - - + +
43F MET* 3.2 20.7 + - - +
44F LEU* 2.9 12.1 + - + +
46F GLN* 1.3 101.2 + - - +
48F LEU* 1.3 59.3 + - - +
50F GLU* 2.8 34.7 + - - +
51F LYS* 3.0 30.3 + - - +
116G GLU* 5.8 1.8 + - - -
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Residues in contact with LEU 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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26F SER* 5.0 6.1 - - - -
29F TYR* 5.8 0.7 - - + -
30F ILE* 4.4 20.6 - - + -
44F LEU* 2.8 24.7 + - + +
45F PHE* 3.1 21.5 + - + +
47F ARG* 1.3 76.6 - - - +
49F GLN* 1.3 52.2 + - - +
51F LYS* 4.4 1.3 - - - +
52F ARG* 2.7 10.2 + - - -
53F MET* 2.6 40.8 + - + +
54F LEU* 3.2 40.5 + - + +
61F PHE* 3.5 33.4 - - + -
62F LEU* 5.6 0.4 - - + -
65F LEU* 4.5 10.5 - - + -
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Residues in contact with GLN 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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125E GLN* 5.1 7.0 - - - +
45F PHE 2.7 16.2 + - - +
46F GLN* 3.4 22.2 - - - +
47F ARG 3.2 0.2 - - - -
48F LEU* 1.3 72.6 - - - +
50F GLU* 1.3 64.7 + - - +
51F LYS 3.2 0.2 - - - -
52F ARG* 3.0 25.0 + - - +
54F LEU 3.3 17.7 + - - +
55F GLU* 2.9 38.1 + - - +
168G ASN* 4.1 4.3 - - - +
170G SER* 4.5 11.0 - - - -
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Residues in contact with GLU 50 (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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30F ILE* 6.4 0.4 - - - -
34F LYS* 3.2 32.1 + - - +
46F GLN 2.8 13.9 + - - +
47F ARG* 2.8 42.7 + - - +
49F GLN* 1.3 76.3 - - - +
51F LYS* 1.3 68.9 + - + +
116G GLU* 4.6 8.8 - - - +
167G ILE* 2.8 29.2 - - - +
168G ASN* 3.1 23.7 - - - +
169G LYS* 2.9 29.1 + - - +
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Residues in contact with LYS 51 (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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29F TYR* 3.7 24.5 + - + +
30F ILE* 3.9 13.7 - - + -
31F PRO* 3.8 25.0 - - - +
34F LYS* 5.8 0.6 - - - +
47F ARG 3.0 18.7 + - - +
48F LEU* 4.2 1.6 - - - +
50F GLU* 1.3 91.0 + - + +
52F ARG* 1.3 69.5 + - - +
53F MET* 3.2 33.7 - - + +
165G ALA 5.4 5.3 + - - -
166G GLN* 5.5 6.9 + - - +
167G ILE 5.2 6.2 + - - +
169G LYS* 3.3 16.1 - - + +
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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