Contacts of the helix formed by residues 38 - 46 (chain D) in PDB entry 1ZXN
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 THR 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C LEU* 3.9 0.7 - - - -
37D LYS* 1.3 77.2 - - - +
39D GLN* 1.3 69.8 + - + +
40D LEU* 3.0 28.9 - - + +
41D GLU* 3.1 32.9 + - + +
42D HIS* 2.9 21.3 + - - +
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Residues in contact with GLN 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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36C LYS* 6.2 2.0 - - - +
39C GLN* 3.6 51.3 - - - +
146C LEU* 3.6 12.4 - - + +
37D LYS 4.0 0.2 + - - -
38D THR* 1.3 76.6 - - + +
40D LEU* 1.3 61.9 + - - +
42D HIS* 3.5 2.0 - - - +
43D ILE* 3.1 30.0 + - + +
50D TYR* 4.8 1.2 + - - -
145D LEU* 3.5 27.6 - - + +
146D LEU* 3.8 22.1 - - - +
165D TYR* 4.9 5.5 + - - +
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Residues in contact with LEU 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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38D THR* 3.0 15.0 - - + +
39D GLN* 1.3 80.7 - - - +
41D GLU* 1.3 64.9 + - + +
42D HIS 3.3 0.7 + - - -
43D ILE* 3.4 3.5 + - + +
44D LEU* 3.4 27.1 + - + +
145D LEU* 4.1 9.5 - - + +
172D ILE* 3.3 38.1 - - + -
197D ASN 3.9 13.2 - - - +
198D MET* 4.3 25.4 - - + +
199D GLY* 4.8 6.3 - - - -
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Residues in contact with GLU 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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36D LYS 4.8 2.3 - - - +
37D LYS* 3.9 29.0 + - + +
38D THR* 3.1 42.3 + - + +
40D LEU* 1.3 79.5 - - + +
42D HIS* 1.3 58.5 + - - +
44D LEU* 3.4 9.2 + - - +
45D LEU* 2.8 29.7 + - - +
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Residues in contact with HIS 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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146C LEU* 3.4 21.2 - - + +
151C TYR* 4.0 16.6 - + - -
163C ASN* 2.8 28.7 + - + -
165C TYR* 3.4 29.8 - + - -
37D LYS* 4.3 7.6 - - + +
38D THR 2.9 17.4 + - - +
39D GLN 3.5 4.9 - - - +
41D GLU* 1.3 72.5 - - - +
43D ILE* 1.3 57.5 + - - +
44D LEU 3.0 1.6 - - - -
45D LEU* 2.8 6.9 + - + -
46D ARG* 2.7 56.8 + - + +
49D THR* 5.7 2.2 - - + -
50D TYR* 2.8 25.2 + + - +
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Residues in contact with ILE 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 GLN* 3.1 16.2 + - + +
40D LEU* 3.4 5.6 + - - +
42D HIS* 1.3 76.2 - - - +
44D LEU* 1.3 56.2 + - - +
47D PRO* 3.2 27.7 - - - +
50D TYR* 3.4 32.3 - - + -
145D LEU* 3.7 23.3 - - + -
165D TYR* 3.6 29.2 - - + +
169D LEU* 3.8 17.3 - - + -
172D ILE* 4.2 13.5 - - + -
173D PHE* 3.7 26.2 - - + -
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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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40D LEU* 3.4 25.7 + - + +
41D GLU* 3.4 10.2 + - - +
42D HIS 3.0 0.4 - - - -
43D ILE* 1.3 76.7 - - - +
45D LEU* 1.3 63.0 + - - +
47D PRO* 3.4 3.6 - - - +
172D ILE* 3.7 30.5 - - + +
173D PHE* 4.0 15.7 - - + -
197D ASN* 4.1 27.6 - - + +
225D LYS* 3.2 31.7 + - + +
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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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151C TYR* 3.6 44.0 - - + +
153C ASP* 4.9 6.4 - - - +
37D LYS* 3.7 31.0 - - + +
41D GLU 2.8 17.4 + - - +
42D HIS* 2.8 7.6 + - + +
44D LEU* 1.3 80.6 - - - +
46D ARG* 1.3 82.4 + - + +
47D PRO* 3.4 5.5 - - - +
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Residues in contact with ARG 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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150C ASN 3.1 12.5 + - - -
151C TYR* 3.7 14.8 + - - +
153C ASP* 2.8 42.8 + - - -
162C ARG* 3.0 38.6 + - - +
163C ASN* 4.7 4.7 - - + +
370C ASN* 6.1 1.6 - - - +
42D HIS* 2.7 41.3 + - + +
43D ILE 3.4 4.0 - - - -
45D LEU* 1.3 91.4 + - + +
47D PRO* 1.3 69.1 - - - +
48D ASP* 3.4 2.9 - - - -
49D THR* 3.2 26.2 + - - +
50D TYR* 3.3 13.8 - - + -
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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