Contacts of the helix formed by residues 36 - 46 (chain D) in PDB entry 1Z6T
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 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.6 2.2 - - - +
33D GLY 6.1 0.7 - - - +
35D LEU* 1.3 78.8 - - - +
37D ILE* 1.3 58.5 + - - +
38D SER* 3.3 11.4 + - - -
39D GLU* 2.9 41.6 + - + +
40D GLU* 2.9 26.3 + - - +
63D LYS* 5.8 0.7 - - - +
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Residues in contact with ILE 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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30D ILE* 4.4 24.2 - - + -
36D THR* 1.3 74.0 - - - +
38D SER* 1.3 58.2 + - - +
40D GLU* 3.4 23.9 + - - +
41D GLU* 2.9 27.4 + - + +
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Residues in contact with SER 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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36D THR* 3.3 9.6 + - - -
37D ILE* 1.3 76.5 - - - +
39D GLU* 1.3 72.0 + - - +
41D GLU* 3.3 20.4 - - - +
42D LYS* 3.0 25.8 + - - +
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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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35D LEU* 3.5 22.2 - - + +
36D THR* 2.9 46.6 + - + +
38D SER* 1.3 85.5 + - - +
40D GLU* 1.3 60.1 + - - +
43D VAL* 3.2 21.2 + - - +
59D MET* 3.3 39.7 - - + +
63D LYS* 3.1 33.0 + - - -
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Residues in contact with GLU 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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23D SER 4.9 1.4 - - - +
26D MET* 3.8 32.5 - - + +
27D ASP* 3.7 14.0 - - - +
30D ILE* 3.1 31.2 - - + +
35D LEU* 4.6 2.4 - - + +
36D THR 2.9 12.5 + - - +
37D ILE* 3.5 24.6 - - - +
39D GLU* 1.3 75.0 - - - +
41D GLU* 1.3 58.6 + - - +
43D VAL* 3.0 4.9 + - - +
44D ARG* 2.9 38.3 + - + +
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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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37D ILE* 2.9 18.0 + - + +
38D SER* 3.3 26.9 + - - +
40D GLU* 1.3 76.2 + - - +
42D LYS* 1.3 62.6 + - - +
44D ARG* 3.3 7.1 + - - +
45D ASN* 3.1 23.9 + - + +
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Residues in contact with LYS 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 SER 3.0 17.6 + - - +
39D GLU 3.6 6.1 - - - +
41D GLU* 1.3 80.1 - - - +
43D VAL* 1.3 61.6 + - - +
45D ASN* 3.5 17.8 + - - +
46D GLU* 3.8 14.4 + - - +
55D MET* 3.7 28.7 - - - +
58D LYS* 5.5 7.1 - - - +
59D MET* 3.7 21.6 - - + +
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Residues in contact with VAL 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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22D THR* 3.9 5.8 - - + +
26D MET* 3.5 34.3 - - + -
39D GLU 3.2 14.1 + - - +
40D GLU 3.0 8.8 + - - +
42D LYS* 1.3 76.4 - - - +
44D ARG* 1.3 60.8 + - - +
46D GLU* 3.1 10.6 + - - +
52D ARG* 3.0 52.1 - - + +
55D MET* 3.7 24.2 - - + -
56D LEU* 4.0 11.4 - - + +
59D MET* 3.8 12.3 - - - -
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Residues in contact with ARG 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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26D MET* 5.3 7.2 - - + -
40D GLU* 2.9 24.7 + - + +
41D GLU* 3.3 7.2 + - - +
43D VAL* 1.3 75.0 - - - +
45D ASN* 1.3 63.8 + - - +
46D GLU 3.3 0.4 + - - -
52D ARG* 3.4 37.8 + - - +
413D ASP* 3.8 42.1 + - - +
416D GLN* 5.7 8.1 - - - +
417D GLU* 4.7 13.1 + - - +
420D ASN* 6.2 0.4 - - - +
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Residues in contact with ASN 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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41D GLU* 3.1 13.6 + - + +
42D LYS* 3.6 14.5 - - - +
43D VAL 3.2 0.2 - - - -
44D ARG* 1.3 77.8 - - - +
46D GLU* 1.3 68.7 + - - +
47D PRO* 3.5 4.9 - - - +
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Residues in contact with GLU 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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304C ALA* 6.1 0.9 - - - +
42D LYS* 3.9 12.0 - - - +
43D VAL 3.1 15.5 + - - +
44D ARG 3.8 1.0 - - - +
45D ASN* 1.3 84.3 + - - +
47D PRO* 1.3 74.4 - - + +
48D THR 3.3 0.6 + - - -
51D GLN* 3.7 33.3 - - - +
52D ARG* 3.3 38.6 + - + +
55D MET* 4.0 28.5 - - + +
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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