Contacts of the helix formed by residues 34 - 45 (chain D) in PDB entry 1XK4
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 GLN 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ASN* 1.3 76.1 - - - +
35D GLY* 1.3 58.0 + - - +
37D PHE* 3.3 2.5 + - + +
38D LYS* 2.9 67.2 + - + +
60D GLU* 3.8 25.2 + - + +
63D MET* 3.6 26.4 - - + +
64D GLU* 5.1 6.7 + - - +
72D LYS 4.3 3.5 + - - +
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Residues in contact with GLY 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 ASN* 3.3 6.2 + - - -
34D GLN* 1.3 78.6 - - - +
36D GLU* 1.3 57.0 + - - +
38D LYS* 3.4 11.5 + - - +
39D GLU* 3.0 30.2 + - - +
42D ARG* 5.5 0.3 + - - -
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Residues in contact with GLU 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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22D TYR* 3.1 31.4 - - + +
25D LYS* 3.7 9.8 - - + +
26D LEU* 2.8 46.3 + - + +
31D THR 3.4 3.5 - - - +
32D LEU* 3.6 11.7 - - + -
33D ASN* 3.0 33.6 + - - +
35D GLY* 1.3 73.7 - - - +
37D PHE* 1.3 64.6 + - - +
39D GLU* 3.2 8.5 + - - +
40D LEU* 3.0 23.9 + - - +
4502D CA 2.8 19.7 - - - -
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Residues in contact with PHE 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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32D LEU* 4.0 21.9 - - + +
33D ASN 2.9 16.6 + - - +
34D GLN* 3.6 4.5 - - + +
36D GLU* 1.3 76.0 - - - +
38D LYS* 1.3 66.4 + - + +
39D GLU 3.3 0.2 + - - -
40D LEU* 3.3 3.1 + - + +
41D VAL* 3.0 48.6 + - + +
49D LEU* 5.8 0.2 - - + -
59D ILE* 3.6 31.2 - - + -
62D ILE* 3.9 21.1 - - + -
63D MET* 3.6 32.8 - - + -
66D LEU* 4.3 4.5 - - + -
74D LEU* 3.7 20.6 - - + -
79D PHE* 4.3 9.0 - + - -
82D LEU* 3.9 19.1 - - + -
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Residues in contact with LYS 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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34D GLN* 2.9 41.0 + - + +
35D GLY* 3.7 9.2 - - - +
36D GLU 3.3 0.2 - - - -
37D PHE* 1.3 77.4 - - + +
39D GLU* 1.3 58.3 + - - +
41D VAL* 3.5 1.6 + - - +
42D ARG* 3.0 36.7 + - - +
53D ASN* 4.9 0.5 - - - +
56D GLU* 2.6 34.7 + - + +
59D ILE* 3.9 23.5 - - + +
60D GLU* 2.5 48.1 + - - +
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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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22D TYR* 3.5 13.5 + - + -
25D LYS* 3.3 36.8 + - - +
35D GLY 3.0 14.5 + - - +
36D GLU* 3.5 11.0 - - - +
37D PHE 3.2 0.2 - - - -
38D LYS* 1.3 74.1 - - - +
40D LEU* 1.3 65.5 + - - +
42D ARG* 3.3 32.6 + - - +
43D LYS* 3.1 39.2 + - - +
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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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5B LEU* 4.3 12.1 - - + -
18D THR* 4.0 15.9 - - + +
19D PHE* 4.3 4.3 - - - -
22D TYR* 3.7 37.2 - - + -
32D LEU* 4.2 13.0 - - + -
36D GLU 3.0 16.5 + - - +
37D PHE* 3.7 5.6 - - + +
39D GLU* 1.3 78.6 - - - +
41D VAL* 1.3 62.7 + - + +
44D ASP* 2.8 31.3 + - - +
45D LEU* 4.1 17.9 - - + -
79D PHE* 3.9 37.9 - - + -
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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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37D PHE* 3.0 54.6 + - + +
38D LYS 4.0 3.4 - - - +
40D LEU* 1.3 76.8 - - + +
42D ARG* 1.3 63.5 + - - +
45D LEU* 3.2 35.3 + - + -
49D LEU* 3.7 24.2 - - + -
53D ASN* 3.1 36.8 + - - +
59D ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 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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35D GLY 5.5 0.6 + - - -
38D LYS* 3.0 20.6 + - - +
39D GLU* 3.7 35.8 + - - +
40D LEU 3.3 0.4 - - - -
41D VAL* 1.3 77.5 - - - +
43D LYS* 1.3 86.4 + - - +
46D GLN* 3.2 23.2 + - - +
53D ASN* 3.5 18.4 + - + +
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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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3B THR* 3.6 4.3 - - - +
22D TYR* 3.9 20.6 - - - +
39D GLU* 3.1 29.2 + - - +
42D ARG* 1.3 104.0 - - + +
44D ASP* 1.3 66.7 + - - +
45D LEU 3.4 1.1 + - - -
46D GLN* 3.0 30.4 + - - +
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Residues in contact with ASP 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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3B THR* 2.8 29.7 + - - -
5B LEU* 3.7 25.9 + - + +
6B GLU* 3.6 1.6 - - - +
18D THR* 3.5 14.6 + - + +
21D GLN* 5.0 1.4 + - - -
22D TYR* 2.9 43.1 + - - -
40D LEU* 2.8 19.0 + - + +
43D LYS* 1.3 74.5 - - - +
45D LEU* 1.3 66.9 + - - +
46D GLN 3.6 0.7 - - - -
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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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5B LEU* 3.6 18.8 - - + -
6B GLU* 3.2 17.7 - - + -
9B LEU* 4.7 4.0 - - + -
40D LEU* 3.6 15.2 + - + -
41D VAL* 3.2 19.3 + - + +
44D ASP* 1.3 85.0 - - - +
46D GLN* 1.3 58.8 + - - +
47D ASN 3.1 3.8 - - - -
48D PHE* 4.3 7.6 - - + -
49D LEU* 2.9 49.0 + - + +
53D ASN* 3.5 2.3 + - - -
82D LEU* 4.0 13.9 - - + -
83D MET* 4.1 8.3 - - + -
86D LEU* 3.8 32.3 - - + -
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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