Contacts of the helix formed by residues 34 - 41 (chain D) in PDB entry 5L1Z
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 CYS 34 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN* 3.7 18.6 - - - +
1D MET* 3.4 27.1 - - + +
18D PRO* 4.6 5.4 - - + -
22D CYS* 4.0 5.6 - - - -
32D PHE 4.2 0.7 - - - -
33D HIS* 1.3 83.8 - - + +
35D GLN* 1.3 66.2 + - - +
36D VAL* 3.5 12.1 - - - -
37D CYS* 3.3 19.6 - - - +
38D PHE* 3.3 17.2 + - - +
101D ZN 2.4 34.1 - - - -
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Residues in contact with GLN 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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46B GLN* 3.4 41.5 - - + +
50B GLN* 4.5 2.3 - - - +
176B PHE* 4.0 7.5 - - - -
179B THR* 3.0 29.9 - - + +
180B ASN* 3.3 22.0 + - - +
183B HIS* 3.5 14.3 - - + +
0D ACE 3.9 11.9 - - + +
1D MET* 3.8 11.7 - - + +
34D CYS* 1.3 75.0 - - - +
36D VAL* 1.3 64.4 + - - +
38D PHE* 3.5 3.8 + - - +
39D ILE* 3.0 59.8 + - + +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN* 4.0 13.7 - - - +
46B GLN* 3.8 11.9 - - + -
47B ASP* 3.7 38.4 - - + +
50B GLN* 2.9 27.8 - - - +
22D CYS* 5.8 2.5 - - - -
34D CYS* 3.4 6.8 - - - -
35D GLN* 1.3 75.0 - - - +
37D CYS* 1.3 56.1 + - - +
39D ILE* 3.1 1.3 + - - -
40D THR* 2.7 60.2 + - + +
47D TYR* 6.5 0.2 - - + -
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Residues in contact with CYS 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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22D CYS* 4.4 5.8 - - - -
23D THR 5.0 0.2 - - - -
30D CYS 3.4 18.4 - - - +
31D CYS 3.6 2.7 - - - +
33D HIS* 3.8 9.9 - - - -
34D CYS* 3.3 10.7 - - - +
36D VAL* 1.3 82.1 - - - +
38D PHE* 1.3 56.8 + - - +
40D THR* 3.5 6.7 - - - -
41D LYS* 2.6 62.1 + - + +
101D ZN 2.4 37.7 - - - -
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Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 3.5 27.1 - + + -
177B MET* 6.2 0.7 - - + -
180B ASN* 3.1 32.5 - - + -
184B LEU* 5.1 1.6 - - + -
245B LEU* 5.5 3.4 - - + -
252B LEU* 4.7 1.8 - - + -
56C LEU* 4.2 22.9 - - + -
31D CYS 3.1 18.8 + - - +
32D PHE* 3.8 29.4 - + - -
34D CYS 3.3 15.0 + - - +
35D GLN* 3.7 4.3 - - - +
36D VAL 3.2 0.6 - - - -
37D CYS* 1.3 78.4 - - - +
39D ILE* 1.3 64.9 + - + +
42D ALA* 3.0 29.8 - - + +
43D LEU* 2.9 49.0 + - + +
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Residues in contact with ILE 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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39B GLN 5.0 2.2 - - - +
43B ASN* 4.0 21.8 - - + +
46B GLN* 6.2 0.7 - - + -
180B ASN* 4.3 2.5 - - - +
183B HIS* 4.1 23.1 - - + +
184B LEU* 4.4 4.0 - - + -
35D GLN* 3.0 41.7 - - + +
36D VAL* 3.1 4.6 + - - +
38D PHE* 1.3 83.9 - - + +
40D THR* 1.3 52.3 + - - +
43D LEU* 3.4 25.7 - - + +
44D GLY 3.0 6.1 + - - -
45D ILE* 2.5 62.0 + - + +
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Residues in contact with THR 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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43B ASN* 3.2 26.2 - - - +
250B ASN* 4.3 0.2 + - - -
26D TYR* 4.1 9.2 + - - -
36D VAL* 2.7 44.0 + - + +
37D CYS* 3.5 8.0 - - - -
39D ILE* 1.3 75.7 - - - +
41D LYS* 1.3 65.6 + - - +
44D GLY* 3.0 18.4 - - - -
45D ILE 3.5 9.2 - - - +
46D SER* 4.9 7.5 - - - -
47D TYR* 6.3 0.9 - - + -
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Residues in contact with LYS 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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250B ASN* 3.6 11.4 + - - -
251B ARG* 3.6 19.4 + - - -
23D THR* 3.3 25.4 + - - -
24D ASN* 5.2 2.5 - - - +
25D CYS 3.1 31.1 + - - +
26D TYR* 3.4 28.0 - - + -
30D CYS* 3.7 24.9 + - - +
31D CYS* 4.3 12.1 - - - -
37D CYS* 2.6 39.9 + - + +
40D THR* 1.3 80.3 - - - +
42D ALA* 1.3 63.4 + - - +
33N G 4.0 8.7 - - - +
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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