Contacts of the helix formed by residues 50 - 65 (chain E) in PDB entry 2F4V
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 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C ARG* 5.0 15.2 + - - +
135C LYS* 4.1 25.6 - - + +
168C ALA* 5.2 8.0 - - - +
28E PHE* 4.4 0.7 - - - -
48E ALA 2.7 8.3 + - - -
49E PRO* 1.3 89.3 - - + +
51E VAL* 1.3 72.2 + - - +
52E PRO* 3.4 4.3 - - + -
53E LEU* 2.7 48.0 + - + +
54E ALA* 2.8 8.3 + - - +
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E MET* 6.4 0.7 - - + -
13E ILE* 4.5 24.0 - - + -
28E PHE* 3.9 43.9 - - + -
50E GLU* 1.3 66.5 - - - +
52E PRO* 1.3 66.4 - - + +
54E ALA* 2.4 40.8 + - + +
55E VAL* 3.2 8.7 + - + +
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Residues in contact with PRO 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS* 6.1 2.5 - - - +
50E GLU* 3.9 4.3 - - + -
51E VAL* 1.3 99.3 - - + +
53E LEU* 1.3 57.2 + - - +
54E ALA 2.5 12.1 + - - -
55E VAL* 3.2 10.2 + - + +
56E GLN* 3.0 30.1 + - - +
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A G 4.4 21.8 - - - +
1073A U 5.6 3.4 - - - +
48E ALA* 5.0 8.3 - - + +
49E PRO* 5.0 1.6 - - + -
50E GLU* 2.7 53.8 + - + +
52E PRO* 1.3 75.6 - - - +
54E ALA* 1.3 58.2 + - - +
56E GLN* 3.3 14.5 - - + +
57E LYS* 3.2 29.6 + - + +
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Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 5.7 0.9 - - + -
28E PHE* 4.4 9.9 - - + +
29E GLY 4.8 0.4 - - - -
30E ALA* 4.1 5.4 - - + -
46E GLY* 3.3 27.2 - - - +
47E LYS 4.7 0.2 - - - -
48E ALA 4.2 13.7 - - - +
50E GLU 2.8 5.1 + - - +
51E VAL* 2.4 39.0 + - + +
52E PRO 2.5 0.2 + - - -
53E LEU* 1.3 64.1 - - - +
55E VAL* 1.3 57.7 + - + +
56E GLN 3.1 0.4 - - - -
57E LYS* 2.5 28.8 + - - +
58E ALA 2.8 11.8 + - - -
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Residues in contact with VAL 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU* 4.5 13.5 - - - +
10E MET* 4.0 35.7 - - + -
13E ILE* 4.9 4.5 - - + -
30E ALA* 3.7 14.8 - - + +
32E VAL* 4.0 18.9 - - + +
51E VAL* 3.4 18.6 - - + +
52E PRO* 3.5 14.6 - - + +
54E ALA* 1.3 71.9 - - + +
56E GLN* 1.3 66.2 + - - +
58E ALA* 3.0 2.1 - - - +
59E GLY* 2.7 23.9 + - - -
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Residues in contact with GLN 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU* 4.8 11.1 + - - +
52E PRO* 3.0 21.5 + - - +
53E LEU* 3.3 17.4 - - + +
55E VAL* 1.3 79.9 - - - +
57E LYS* 1.3 62.2 + - - +
59E GLY* 3.1 9.2 + - - -
60E TYR* 3.2 11.5 + - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A G 5.0 5.9 + - - -
1073A U 3.2 42.8 + - - +
46E GLY* 4.6 4.7 - - - -
47E LYS 2.9 26.5 + - - +
48E ALA* 3.8 12.9 - - - +
53E LEU* 3.5 16.6 - - + +
54E ALA* 2.5 15.3 + - - +
56E GLN* 1.3 73.1 - - + +
58E ALA* 1.3 71.3 + - - +
60E TYR* 2.8 17.8 + - + +
61E TYR* 3.0 47.5 + - + +
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Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ALA* 3.9 4.7 - - + +
32E VAL* 3.2 25.4 - - + -
44E GLY* 3.9 4.8 - - - +
45E PHE 4.2 4.0 - - - -
46E GLY* 3.5 30.6 - - - +
54E ALA 2.8 10.4 + - - +
55E VAL* 3.0 12.3 - - - +
57E LYS* 1.3 69.2 - - - +
59E GLY* 1.3 69.3 + - - +
61E TYR* 2.6 17.4 + - - +
62E ALA* 2.7 11.5 + - - -
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Residues in contact with GLY 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU* 4.0 16.4 - - - -
32E VAL* 4.1 9.4 - - - +
55E VAL 2.7 16.1 + - - -
56E GLN 3.3 5.8 - - - -
58E ALA* 1.3 69.7 - - - +
60E TYR* 1.3 54.2 + - - +
62E ALA* 2.5 37.9 + - - +
63E ARG* 3.1 20.0 + - - -
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Residues in contact with TYR 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A U 5.6 1.7 + - - -
1074A G 4.5 17.8 + - - -
56E GLN 3.2 8.4 + - - +
57E LYS* 2.8 17.8 + - - +
59E GLY* 1.3 71.7 - - - +
61E TYR* 1.3 71.4 + + + +
63E ARG* 3.4 18.9 + - - +
64E ARG* 3.0 66.2 + - + +
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A U 4.8 0.3 + - - -
1074A G 2.4 40.4 + - - -
1075A C 5.3 5.6 - - - -
43E LEU 4.4 2.7 - - - +
44E GLY* 4.5 8.3 - - - -
45E PHE 4.5 15.7 - - - +
46E GLY* 5.6 0.7 - - - -
47E LYS 6.2 0.2 - - - -
57E LYS* 3.0 61.1 + - + +
58E ALA* 2.6 14.3 + - - +
60E TYR* 1.3 80.0 - + + +
62E ALA* 1.3 69.5 + - - +
64E ARG* 3.0 15.2 + - + +
65E ASN* 3.2 12.5 + - - +
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 4.5 5.6 - - + +
34E VAL* 3.2 28.5 - - + -
42E GLY* 4.1 1.4 - - - -
43E LEU 3.6 14.6 - - - -
44E GLY* 3.7 12.6 - - - +
58E ALA 2.7 7.6 + - - +
59E GLY* 2.5 23.5 + - - +
61E TYR* 1.3 76.9 - - - +
63E ARG* 1.3 52.7 + - - +
64E ARG 2.7 12.6 + - - -
65E ASN* 2.9 22.3 + - - +
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PHE* 4.8 23.0 - - + +
8E GLU* 3.1 42.4 + - - +
34E VAL* 3.8 20.7 - - + +
59E GLY* 3.1 21.5 + - - -
60E TYR* 4.1 11.4 - - - +
61E TYR 3.3 0.8 - - - -
62E ALA* 1.3 77.5 - - - +
64E ARG* 1.3 66.7 + - + +
66E MET* 3.1 42.9 - - + +
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E TYR* 3.0 70.2 + - + +
61E TYR* 3.6 9.0 - - + +
62E ALA 2.7 6.3 + - - -
63E ARG* 1.3 83.7 - - - +
65E ASN* 1.3 57.2 + - - +
66E MET* 3.5 6.9 + - - +
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E VAL 3.8 0.5 - - - +
42E GLY* 3.7 12.5 - - - -
43E LEU* 3.7 32.5 + - - +
61E TYR 3.2 6.1 + - - +
62E ALA 2.9 15.6 + - - +
64E ARG* 1.3 73.8 - - - +
66E MET* 1.3 59.5 + - - +
67E VAL 4.1 0.3 + - - -
133E TYR* 5.9 4.0 - - - -
136E MET* 4.0 4.3 - - - +
140E ARG* 2.9 33.1 + - - +
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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