Contacts of the helix formed by residues 32 - 42 (chain D) in PDB entry 5LXM
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 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A HIS 3.3 14.2 - - - +
189A ARG* 3.7 6.9 - - - +
246A TYR* 2.7 35.4 + - - +
250A LYS* 3.6 23.3 - - + +
29D GLN* 2.9 39.9 + - - +
30D ASN* 2.7 0.4 + - - -
31D ILE* 1.3 79.7 - - - +
33D SER* 1.3 57.9 + - - +
34D TRP 3.0 7.3 + - - -
35D PHE* 3.1 19.3 + - + -
36D GLU* 3.0 14.2 - - - +
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Residues in contact with SER 33 (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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250A LYS* 5.2 1.2 + - - +
30D ASN* 2.1 53.3 + - - -
31D ILE* 5.4 0.2 - - - -
32D ASP* 1.3 65.2 - - - +
34D TRP* 1.3 62.9 + - - +
35D PHE 3.1 0.6 + - - -
36D GLU* 3.2 16.4 + - - +
37D MK8 2.9 24.3 + - - +
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Residues in contact with TRP 34 (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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183A GLU* 3.7 44.2 - - + -
184A ILE* 4.3 6.1 - - + -
187A HIS* 3.3 44.2 - + + -
280A HIS* 5.2 4.9 - + + -
11D ASP* 2.7 28.1 + - - -
31D ILE* 3.2 16.5 + - + +
32D ASP 3.0 0.4 - - - -
33D SER* 1.3 77.5 - - - +
35D PHE* 1.3 83.0 + + - +
37D MK8 3.4 16.4 - - + +
38D LYS* 2.9 64.9 + - + +
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Residues in contact with PHE 35 (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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184A ILE* 3.4 33.9 - - + -
187A HIS* 3.5 30.5 - - + -
188A LEU* 3.5 22.0 - - + -
250A LYS* 4.0 20.0 - - + +
252A VAL* 3.5 26.7 - - + -
280A HIS* 3.1 35.5 + + + +
32D ASP* 3.1 25.0 + - + +
33D SER 3.1 0.6 - - - -
34D TRP* 1.3 94.0 - + - +
36D GLU* 1.3 69.3 + - - +
38D LYS 3.3 0.9 + - - -
39D ALA* 3.0 20.1 + - - +
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Residues in contact with GLU 36 (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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249A SER 4.4 6.4 - - - +
250A LYS* 3.1 33.7 + - - +
32D ASP 3.0 20.8 - - - +
33D SER* 3.2 14.0 + - - +
35D PHE* 1.3 73.8 - - - +
37D MK8 1.3 69.8 + - + +
39D ALA* 3.2 8.2 + - - +
40D ASN* 3.2 26.5 + - - +
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Residues in contact with MK8 37 (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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33D SER 2.9 17.1 + - - +
34D TRP* 3.4 21.3 - - + +
36D GLU* 1.3 81.2 + - + +
38D LYS* 1.3 60.3 + - + +
40D ASN* 3.2 19.3 + - + +
41D MK8 1.3 95.6 + - + +
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Residues in contact with LYS 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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183A GLU* 4.7 6.9 + - - -
280A HIS* 4.3 5.4 - - + -
506A MES 3.4 13.5 - - - +
11D ASP* 3.8 11.1 + - - +
34D TRP* 2.9 66.1 + - + +
35D PHE 3.6 4.7 - - - +
36D GLU 3.3 0.2 - - - -
37D MK8 1.3 76.0 + - + +
39D ALA* 1.3 65.4 + - - +
41D MK8 4.2 14.0 - - + +
42D GLU* 3.1 56.6 + - + +
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Residues in contact with ALA 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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280A HIS* 4.5 0.7 - - + +
282A PRO* 3.7 28.3 - - + -
283A SER* 5.8 1.1 - - - +
506A MES 3.6 11.4 - - - -
35D PHE 3.0 12.9 + - - +
36D GLU* 3.2 11.4 + - - +
38D LYS* 1.3 76.0 - - - +
40D ASN* 1.3 61.6 + - - +
43D ASN* 3.1 6.8 + - - -
101D NH3 2.8 27.9 + - - -
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Residues in contact with ASN 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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36D GLU* 3.2 17.1 + - - +
37D MK8 3.7 18.8 - - + +
39D ALA* 1.3 78.8 - - - +
41D MK8 1.3 73.6 + - + +
43D ASN* 3.0 15.1 + - - +
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Residues in contact with MK8 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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37D MK8 1.3 82.6 + - + +
38D LYS* 3.8 17.0 - - + +
40D ASN* 1.3 79.5 + - + +
42D GLU* 1.3 65.0 + - + +
43D ASN* 3.5 1.7 + - - +
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Residues in contact with GLU 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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506A MES 3.2 51.5 - - - +
38D LYS* 3.1 43.5 + - + +
41D MK8 1.3 82.9 + - + +
43D ASN* 1.3 71.5 + - - +
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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