Contacts of the helix formed by residues 40 - 49 (chain D) in PDB entry 1R4N
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 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D SER* 2.9 10.0 + - - +
39D THR* 1.3 83.5 - - + +
41D SER* 1.3 66.3 + - - +
42D LEU 2.8 4.8 + - - -
43D GLN* 3.1 20.4 + - + +
44D PHE* 3.2 32.3 + - + +
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Residues in contact with SER 41 (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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24D LEU* 4.0 25.0 + - - +
35D PHE* 5.7 1.2 - - - -
36D GLU 3.7 8.7 + - - -
38D SER* 3.5 35.2 + - - -
39D THR 3.5 0.2 - - - -
40D GLU* 1.3 75.7 - - - +
42D LEU* 1.3 63.9 + - - +
44D PHE* 3.3 9.2 - - - +
45D LEU* 3.2 18.5 + - - +
312D THR* 6.1 0.2 - - - +
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Residues in contact with LEU 42 (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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17D TRP* 3.5 37.0 - - + -
20D VAL* 4.5 9.4 - - + -
21D LYS* 4.0 31.0 - - + +
24D LEU* 3.9 24.5 - - + +
25D GLU* 6.4 1.8 - - + -
38D SER 4.9 0.2 + - - -
39D THR 4.5 7.3 + - - +
40D GLU 2.8 4.6 + - - +
41D SER* 1.3 72.0 - - - +
43D GLN* 1.3 69.5 + - - +
44D PHE 3.0 1.3 - - - -
45D LEU* 2.8 26.5 + - + +
46D LEU* 3.0 31.9 + - + -
71D GLY* 4.7 5.6 - - - -
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Residues in contact with GLN 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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39D THR 5.2 1.5 + - - +
40D GLU* 3.1 15.2 + - + +
42D LEU* 1.3 78.1 - - - +
44D PHE* 1.3 63.9 + - - +
46D LEU* 3.1 13.7 + - - +
47D ASP* 2.9 57.1 + - - +
73D ARG* 4.3 13.3 - - - +
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Residues in contact with PHE 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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40D GLU* 3.2 26.7 + - + +
41D SER* 3.3 14.1 - - - +
42D LEU 3.0 0.2 - - - -
43D GLN* 1.3 77.3 - - - +
45D LEU* 1.3 68.3 + - - +
47D ASP* 2.8 6.1 + - - -
48D THR* 2.7 63.0 + - + -
49D CYS* 6.3 0.4 - - + -
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Residues in contact with LEU 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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24D LEU* 4.5 3.8 - - + -
41D SER 3.2 8.2 + - - +
42D LEU* 2.8 21.6 + - + +
44D PHE* 1.3 80.7 - - - +
46D LEU* 1.3 60.4 + - - +
47D ASP 3.2 0.2 + - - -
49D CYS* 3.3 38.7 + - + +
70D SER 4.2 0.9 - - - +
71D GLY* 3.1 35.0 - - - +
72D PHE* 3.8 30.1 - - + -
73D ARG 4.8 2.8 + - - -
308D PHE* 4.2 14.1 - - + -
311D ALA* 4.0 17.0 - - + +
312D THR* 3.9 24.7 - - + -
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Residues in contact with LEU 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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17D TRP* 4.0 23.6 - - + +
42D LEU* 3.0 40.4 + - + +
43D GLN* 3.4 18.8 - - - +
45D LEU* 1.3 76.8 - - - +
47D ASP* 1.3 62.6 + - - +
71D GLY* 3.3 31.4 - - - +
72D PHE 4.2 0.4 - - - +
73D ARG* 2.9 74.0 - - + +
74D GLN* 3.7 5.8 - - - +
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Residues in contact with ASP 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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43D GLN* 2.9 46.1 + - - +
44D PHE* 2.8 11.7 + - - +
46D LEU* 1.3 77.5 - - - +
48D THR* 1.3 65.2 + - + +
49D CYS 3.8 0.4 - - - -
73D ARG* 4.4 5.4 + - - -
74D GLN* 3.4 23.8 - - - +
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Residues in contact with THR 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 PHE* 2.7 66.3 + - + +
45D LEU* 4.8 0.2 - - - -
47D ASP* 1.3 80.7 - - + +
49D CYS* 1.3 58.7 + - - +
50D LYS* 3.2 14.9 + - - +
74D GLN* 4.8 0.6 - - - +
139D HIS* 3.3 12.9 + - - -
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Residues in contact with CYS 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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45D LEU* 3.3 32.8 + - + +
47D ASP 3.8 0.4 - - - -
48D THR* 1.3 76.5 + - - +
50D LYS* 1.3 60.3 + - - +
51D VAL* 3.8 7.7 + - - +
72D PHE* 4.2 15.0 - - + -
73D ARG 5.1 0.3 + - - -
74D GLN* 3.4 22.5 + - - +
139D HIS* 3.4 27.8 - - - -
140D ILE* 4.8 0.7 - - - -
311D ALA* 4.1 27.8 - - - -
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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