Contacts of the helix formed by residues 24 - 32 (chain D) in PDB entry 1JLH
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 ASN 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D SER 5.1 0.4 - - - +
22D GLU 2.9 6.2 + - - +
23D LEU* 1.3 75.4 - - - +
25D LEU* 1.3 66.0 + - - +
26D ARG* 3.1 13.6 + - - +
27D ARG* 3.1 51.6 + - - +
28D LEU* 2.9 27.9 + - - +
470D ASN* 3.2 17.8 + - - +
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Residues in contact with LEU 25 (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 ASN* 1.3 70.5 - - - +
26D ARG* 1.3 62.1 + - - +
28D LEU* 3.3 5.0 + - + -
29D PHE* 3.1 36.5 + - + -
35D ARG* 4.6 3.6 - - - +
56D LYS* 3.6 27.1 - - - +
57D ASN 3.4 32.3 - - - +
58D LEU* 3.8 10.0 - - + +
436D MET* 3.4 44.4 - - + +
470D ASN* 2.7 35.4 + - - +
471D ARG 3.9 7.4 - - - +
472D PRO* 4.1 2.2 - - + -
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Residues in contact with ARG 26 (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 ASN* 3.1 11.2 + - - +
25D LEU* 1.3 78.0 - - - +
27D ARG* 1.3 60.5 + - + +
29D PHE* 3.8 1.9 - - - -
30D ASP* 2.5 44.5 + - - +
436D MET* 4.4 6.2 + - - +
437D ARG* 2.8 68.7 + - + +
438D GLY 3.2 19.2 + - - -
439D LYS* 4.3 0.4 - - - +
440D SER* 5.4 5.1 + - - -
443D GLU* 3.1 33.7 + - - -
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Residues in contact with ARG 27 (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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21D SER 3.2 19.8 + - - -
22D GLU* 3.1 31.0 + - - +
24D ASN* 3.1 29.0 + - + +
26D ARG* 1.3 81.3 - - + +
28D LEU* 1.3 63.1 + - + +
30D ASP* 3.8 7.1 - - - +
31D ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 28 (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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22D GLU 4.9 6.3 - - - +
23D LEU* 4.5 11.9 - - + -
24D ASN 2.9 36.1 + - - +
25D LEU* 3.6 11.9 - - + +
27D ARG* 1.3 78.7 - - + +
29D PHE* 1.3 57.6 + - - +
31D ALA* 3.4 4.1 + - + +
32D ASN* 3.1 29.8 + - - +
35D ARG* 3.9 40.8 + - - +
57D ASN 4.7 1.6 - - - +
58D LEU* 5.0 1.1 - - + -
59D VAL 4.1 7.0 - - - +
60D THR* 4.3 17.9 - - + -
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Residues in contact with PHE 29 (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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538C ASP* 4.0 12.8 - - + -
539C ALA* 4.0 22.1 + - + +
540C SER* 3.6 29.2 - - - -
25D LEU* 3.1 30.9 + - + +
26D ARG* 4.0 2.7 - - - +
28D LEU* 1.3 72.1 - - - +
30D ASP* 1.3 68.4 + - - +
31D ALA 3.1 2.2 + - - -
32D ASN 3.0 22.6 + - - +
33D LYS* 4.1 2.8 + - - -
35D ARG* 3.3 37.0 - - + +
36D PHE 4.6 0.4 - - - -
55D SER* 3.2 36.1 - - - -
56D LYS* 4.0 7.4 - - + -
436D MET* 3.5 26.5 - - + -
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Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D ARG* 2.5 39.5 + - - +
27D ARG* 3.8 8.1 - - - +
29D PHE* 1.3 79.9 - - - +
31D ALA* 1.3 59.0 + - - +
32D ASN 5.4 0.2 - - - -
33D LYS 5.6 0.2 - - - -
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Residues in contact with ALA 31 (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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27D ARG 3.0 18.1 + - - +
28D LEU* 3.9 4.3 - - - +
30D ASP* 1.3 80.4 - - - +
32D ASN* 1.3 58.6 + - + +
33D LYS 4.1 1.4 + - - -
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Residues in contact with ASN 32 (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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539C ALA* 4.7 2.6 - - - +
28D LEU 3.1 14.9 + - - +
29D PHE* 3.0 14.8 + - - +
31D ALA* 1.3 79.4 - - + +
33D LYS* 1.3 62.1 + - - +
34D ASP* 2.7 34.3 + - - +
35D ARG* 2.9 34.9 + - + +
38D HIS* 3.2 27.0 + - - -
39D PHE* 4.8 6.3 - - - -
61D GLU* 6.4 0.4 - - - +
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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