Contacts of the helix formed by residues 42 - 51 (chain D) in PDB entry 3EXG
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 GLY 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ASP* 2.8 17.4 + - - -
40D SER 3.3 0.8 + - - -
41D ARG* 1.3 75.0 - - - +
43D LEU* 1.3 63.9 + - - +
44D TRP 3.3 3.8 - - - +
45D LYS* 3.5 25.0 + - - +
46D LYS* 3.3 22.2 + - - +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASN* 3.7 19.1 - - - +
13D MET* 3.8 29.8 - - + -
14D ASP* 4.2 17.3 - - + -
17D LEU* 4.4 12.6 - - + -
25D LEU* 4.2 8.1 - - + -
40D SER* 3.2 31.3 + - - +
41D ARG 3.1 16.0 - - - +
42D GLY* 1.3 75.9 - - - +
44D TRP* 1.3 67.0 + - - +
46D LYS* 3.2 2.7 + - + -
47D TYR* 2.9 36.2 + - + -
52D ILE* 3.5 18.3 - - + +
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Residues in contact with TRP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL 5.4 0.6 + - - -
31D ALA* 3.7 42.0 + - + +
32D GLN* 3.3 48.4 - - + -
40D SER 4.6 1.4 + - - -
42D GLY 3.3 1.4 - - - +
43D LEU* 1.3 79.3 - - - +
45D LYS* 1.3 77.3 + - + +
48D GLY* 2.8 36.1 + - - -
49D ASP* 2.5 37.3 + - - +
52D ILE* 3.7 20.0 - - + +
273E ARG* 3.6 14.9 + - - +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLY* 3.6 24.0 - - - +
44D TRP* 1.3 90.9 - - + +
46D LYS* 1.3 56.9 + - - +
267E ASP* 3.5 37.8 + - - +
269E GLY* 3.8 18.7 - - - +
270E VAL* 3.7 19.9 - - + +
273E ARG* 3.3 31.4 + - - +
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP* 2.9 25.1 + - - +
18D GLU* 3.3 22.1 + - - -
42D GLY 3.3 14.0 + - - +
43D LEU* 3.2 6.0 + - + +
44D TRP 3.0 1.0 - - - -
45D LYS* 1.3 81.2 - - - +
47D TYR* 1.3 91.6 + - + +
48D GLY 3.8 0.4 - - - -
269E GLY* 3.9 22.0 - - - +
272E TYR* 3.6 37.3 - - + +
273E ARG* 3.6 16.7 - - - +
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Residues in contact with TYR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP* 2.9 38.1 + - - -
17D LEU* 3.6 41.5 - - + -
18D GLU* 3.4 8.3 + - - +
43D LEU* 2.9 27.5 + - + +
46D LYS* 1.3 109.5 - - + +
48D GLY* 1.3 65.1 + - - +
50D LYS* 4.7 1.7 + - - +
51D ARG* 3.4 50.5 - - + +
52D ILE* 4.2 4.7 - - + -
272E TYR* 4.1 21.8 - + - -
273E ARG* 4.4 6.0 - - - +
276E GLU* 5.1 0.9 - - - -
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Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D TRP* 2.8 26.2 + - - -
46D LYS 3.8 0.6 - - - -
47D TYR* 1.3 78.0 - - - +
49D ASP* 1.3 59.4 + - - -
50D LYS 3.2 1.3 - - - -
51D ARG 3.1 4.2 + - - -
52D ILE* 3.0 26.9 + - - +
273E ARG* 4.0 21.4 - - - +
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 5.6 0.3 - - - +
44D TRP* 2.5 38.5 + - - -
48D GLY* 1.3 69.3 - - - -
50D LYS* 1.3 67.5 + - - +
52D ILE 4.2 8.5 - - - +
53D ILE* 3.8 16.5 - - - +
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 6.1 0.2 - - - +
153C LYS 5.1 1.8 - - - -
154C TYR* 2.8 74.2 + - + +
21D GLU* 6.0 3.4 - - - +
24D PHE* 4.5 0.7 - - - +
47D TYR 5.1 1.3 - - - +
48D GLY 3.2 0.6 - - - -
49D ASP* 1.3 83.4 - - - +
51D ARG* 1.3 72.1 + - + +
53D ILE* 3.7 14.7 - - - +
280E GLU* 6.3 1.9 - - - -
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C TYR* 3.2 24.4 + - - -
17D LEU* 2.9 39.4 + - + +
20D ASP 3.1 9.5 + - - -
21D GLU* 3.6 17.0 - - - +
23D VAL 2.8 27.3 + - - -
24D PHE* 3.3 6.5 - - + +
25D LEU 2.7 32.7 + - - +
47D TYR* 3.4 46.4 - - + +
48D GLY 3.1 2.0 + - - -
50D LYS* 1.3 90.3 - - + +
52D ILE* 1.3 61.2 + - + +
53D ILE* 3.9 0.9 - - - -
272E TYR* 5.7 0.2 + - - -
276E GLU* 5.2 7.5 + - - -
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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