Contacts of the helix formed by residues 37 - 47 (chain D) in PDB entry 3I6A
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 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ILE* 3.5 10.3 - - - +
36D LYS* 1.3 82.0 - - - +
38D ALA* 1.3 62.3 + - - +
39D GLU* 3.4 17.1 + - - +
40D ASP* 3.2 26.8 + - - -
41D LEU 3.4 15.6 + - - -
218D ASN* 4.6 5.4 - - - -
219D ILE* 3.6 13.5 - - - +
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Residues in contact with ALA 38 (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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37D SER* 1.3 74.3 - - - +
39D GLU* 1.3 73.2 + - - +
41D LEU* 3.5 3.9 + - - +
42D ASP* 2.8 39.6 + - - +
218D ASN* 4.4 6.5 + - - +
219D ILE* 3.2 37.0 - - - +
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Residues in contact with GLU 39 (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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37D SER* 3.2 14.6 - - - +
38D ALA* 1.3 97.3 + - - +
40D ASP* 1.3 65.7 + - - +
42D ASP* 3.7 11.4 - - + +
43D LYS* 2.9 25.1 + - - +
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Residues in contact with ASP 40 (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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34D PHE 3.9 5.3 - - - +
35D ILE* 3.8 17.0 - - + -
36D LYS* 2.8 29.5 + - - +
37D SER* 3.2 21.2 + - - +
39D GLU* 1.3 79.6 - - - +
41D LEU* 1.3 65.4 + - - +
43D LYS* 3.4 12.3 + - - +
44D LEU* 3.4 17.3 + - - +
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Residues in contact with LEU 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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10D PHE* 5.1 5.2 - - + -
35D ILE* 3.8 13.3 - - + +
37D SER 3.4 10.0 + - - +
38D ALA 3.6 8.3 - - - +
39D GLU 3.3 0.2 - - - -
40D ASP* 1.3 79.9 - - - +
42D ASP* 1.3 62.5 + - - +
44D LEU* 3.2 16.2 + - + +
45D ARG* 3.2 38.9 + - - +
50D LEU* 3.7 24.9 - - + -
53D GLN 4.6 2.7 - - - +
54D GLN* 5.5 0.2 - - - -
55D VAL* 4.3 17.3 - - + +
219D ILE* 4.0 14.6 - - + +
220D PHE* 3.5 34.5 - - + -
5104D GSH 5.4 2.0 - - - +
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Residues in contact with ASP 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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38D ALA* 2.8 38.6 + - - +
39D GLU* 3.2 13.6 + - - +
41D LEU* 1.3 72.5 - - - +
43D LYS* 1.3 56.9 + - - +
45D ARG* 3.5 28.5 + - - +
46D ASN* 2.9 46.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 17.0 + - - +
40D ASP* 3.5 8.5 - - - +
41D LEU 3.2 0.2 - - - -
42D ASP* 1.3 74.8 - - - +
44D LEU* 1.3 68.8 + - + +
46D ASN* 3.8 4.7 - - + +
47D ASP* 2.8 63.8 + - - +
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Residues in contact with LEU 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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8D HIS* 3.9 31.4 - - + +
33D LYS* 6.0 2.0 - - + -
35D ILE* 3.7 33.9 - - + -
40D ASP 3.4 10.3 + - - +
41D LEU* 3.2 8.4 + - - +
43D LYS* 1.3 81.2 - - + +
45D ARG* 1.3 60.4 + - - +
47D ASP* 3.6 4.2 + - - +
48D GLY 3.5 2.1 + - - -
49D TYR* 3.0 42.3 + - + +
50D LEU* 3.8 17.5 - - + -
55D VAL* 4.2 12.8 - - + -
57D MET* 4.2 15.0 - - + -
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Residues in contact with ARG 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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131C ARG* 4.1 6.6 - - - +
41D LEU* 3.2 32.6 + - - +
42D ASP* 3.5 31.6 + - - +
44D LEU* 1.3 80.9 - - - +
46D ASN* 1.3 61.4 + - - +
48D GLY* 3.0 19.9 + - - -
50D LEU* 3.7 18.8 + - + -
53D GLN* 3.0 53.9 + - - +
220D PHE* 4.8 3.4 - - - -
5104D GSH 3.5 28.9 + - - -
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Residues in contact with ASN 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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43A LYS* 3.1 31.8 + - - +
42D ASP* 2.9 35.4 + - - +
43D LYS* 4.1 6.0 - - + +
45D ARG* 1.3 72.4 - - - +
47D ASP* 1.3 60.3 + - - +
48D GLY 3.1 4.9 - - - -
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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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39A GLU 4.4 2.3 - - - +
40A ASP* 4.5 3.6 - - - +
43A LYS* 4.1 17.7 - - - +
43D LYS* 2.8 56.2 + - - +
44D LEU* 3.8 6.0 - - - +
45D ARG 3.3 0.2 - - - -
46D ASN* 1.3 78.2 - - - +
48D GLY* 1.3 59.3 + - - +
49D TYR* 3.5 42.4 - - + -
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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