Contacts of the helix formed by residues 34 - 46 (chain D) in PDB entry 2NZD
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 TYR 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.0 19.1 - + + -
26C PRO* 4.6 12.3 - - + -
29C ARG* 4.7 9.0 - - + -
30C VAL* 4.6 8.1 - - + +
33C LEU* 3.3 28.6 - - + +
55C LEU* 4.7 5.0 - - + +
33D SER* 1.3 77.6 - - - +
35D ALA* 1.3 57.8 + - - +
36D ILE 3.4 2.0 - - - -
37D TYR* 3.1 19.9 + + - +
38D VAL* 2.8 39.3 + - + +
60D ASN* 3.1 28.4 + - - +
63D VAL* 3.9 37.2 - - + -
64D ASN* 3.4 25.8 + - - -
67D PHE* 4.5 14.7 - - - -
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Residues in contact with ALA 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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33D SER* 3.2 20.1 + - - +
34D TYR* 1.3 76.5 - - - +
36D ILE* 1.3 62.7 + - + +
38D VAL 3.1 0.3 + - - -
39D TYR* 2.8 32.3 + - - +
56D MET* 3.3 36.3 - - + +
60D ASN* 5.3 1.9 - - + -
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Residues in contact with ILE 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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33D SER 5.3 0.9 + - - +
34D TYR 5.4 0.2 - - - -
35D ALA* 1.3 79.1 - - + +
37D TYR* 1.3 91.8 + - + +
39D TYR* 3.8 6.1 - - - +
40D LYS* 3.0 47.3 + - - +
47J G 3.7 41.3 - - + +
48J G 4.4 13.0 - - - +
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Residues in contact with TYR 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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24C GLN* 3.0 27.4 - - - +
25C PHE* 3.8 23.1 - - + -
26C PRO* 3.4 41.5 - - + +
29C ARG* 3.6 27.6 + - - -
33D SER 4.4 0.2 - - - -
34D TYR* 3.1 15.8 + + - +
36D ILE* 1.3 102.1 - - + +
38D VAL* 1.3 60.6 + - - +
40D LYS* 3.4 20.5 + - + +
41D VAL* 3.2 27.2 + - - +
-43I A 5.6 0.5 + - - -
47J G 3.4 32.7 + - - -
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 4.3 9.4 - - + -
59C THR* 4.7 4.5 - - - +
63C LEU* 3.6 21.5 - - + +
34D TYR* 2.8 34.0 + - + +
35D ALA 3.6 3.8 - - - +
37D TYR* 1.3 75.7 - - - +
39D TYR* 1.3 57.9 + - - +
41D VAL* 3.2 6.8 + - - +
42D LEU* 2.9 24.2 + - + +
51D ILE* 4.8 2.0 - - + -
56D MET* 3.5 27.4 - - + -
59D MET* 3.9 24.0 - - + -
60D ASN* 5.2 0.7 - - - +
63D VAL* 4.2 17.3 - - + -
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Residues in contact with TYR 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 ALA 2.8 17.2 + - - +
36D ILE* 3.8 7.0 - - - +
38D VAL* 1.3 75.0 - - - +
40D LYS* 1.3 68.7 + - + +
42D LEU* 3.2 14.2 + - + +
43D LYS* 3.1 59.5 + - + +
50D GLY* 5.3 0.9 - - - -
51D ILE* 4.2 19.3 - - + -
56D MET* 4.0 8.5 - - + -
-53I T 4.2 31.6 + - - -
-52I A 5.0 8.2 + - - -
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Residues in contact with LYS 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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24C GLN* 4.0 32.7 + - + +
36D ILE* 3.0 35.5 + - - +
37D TYR* 3.5 27.8 - - + +
39D TYR* 1.3 77.3 - - + +
41D VAL* 1.3 58.4 + - - +
43D LYS* 3.0 22.1 + - - +
44D GLN* 3.3 17.3 + - - +
47J G 5.1 7.3 + - - -
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Residues in contact with VAL 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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24C GLN* 4.3 13.5 - - + -
25C PHE* 3.9 20.2 - - + -
56C GLU* 3.9 17.9 - - + +
59C THR* 4.0 10.3 - - - +
60C ALA* 3.8 35.2 - - + +
63C LEU* 4.4 3.4 - - + -
37D TYR 3.2 14.0 + - - +
38D VAL 3.6 6.3 - - - +
40D LYS* 1.3 73.4 - - - +
42D LEU* 1.3 68.4 + - - +
43D LYS 3.2 0.3 + - - -
44D GLN* 3.3 17.6 + - - +
45D VAL* 3.3 21.6 + - + +
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Residues in contact with LEU 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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63C LEU* 3.7 25.1 - - + +
78C ILE* 4.0 23.6 - - + -
38D VAL* 2.9 15.3 + - + +
39D TYR* 3.2 19.9 + - + +
41D VAL* 1.3 77.7 - - - +
43D LYS* 1.3 58.2 + - - +
45D VAL* 3.4 3.7 + - + +
46D HIS* 3.0 40.9 + - + +
49D THR* 3.4 28.0 - - - +
50D GLY* 3.9 5.4 - - - -
51D ILE* 3.9 34.8 - - + -
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Residues in contact with LYS 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 TYR* 3.1 56.9 + - + +
40D LYS* 3.0 13.0 + - - +
42D LEU* 1.3 77.0 - - - +
44D GLN* 1.3 64.9 + - + +
46D HIS 4.4 0.2 - - - -
47D PRO* 3.2 51.7 + - - +
48D ASP 4.5 1.2 - - - -
49D THR 2.7 32.1 + - - +
50D GLY* 4.4 2.2 - - - +
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Residues in contact with GLN 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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24C GLN* 3.5 37.5 - - - +
56C GLU* 5.0 3.5 - - - +
40D LYS 3.3 11.0 + - - +
41D VAL* 3.3 21.6 + - - +
43D LYS* 1.3 78.0 - - - +
45D VAL* 1.3 62.7 + - + +
47D PRO* 4.6 5.9 - - - +
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 4.5 24.7 - - + +
63C LEU* 4.2 11.0 - - + -
64C GLU* 4.0 30.1 - - + +
41D VAL* 3.3 14.2 + - + +
42D LEU* 3.6 9.6 - - + +
44D GLN* 1.3 85.1 - - + +
46D HIS* 1.3 88.8 + - + +
47D PRO* 3.8 5.6 - - - +
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Residues in contact with HIS 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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63C LEU 3.4 19.7 - - - -
64C GLU* 2.8 36.5 + - - -
67C GLY* 3.6 15.7 - - - -
68C ASN* 3.4 20.6 - - - -
71C ARG* 5.4 10.4 + - - -
42D LEU* 3.0 20.2 + - + +
43D LYS* 4.3 1.2 + - - -
45D VAL* 1.3 88.4 + - + +
47D PRO* 1.3 62.5 - - - +
48D ASP 2.8 10.0 + - - -
49D THR* 3.1 36.1 + - - +
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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