Contacts of the helix formed by residues 44 - 56 (chain D) in PDB entry 2G4D
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 LEU 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.2 8.1 - - + -
38D VAL* 4.6 5.8 - - + -
42D THR 4.9 0.7 - - - +
43D HIS* 1.3 71.3 - - - +
45D LYS* 1.3 63.2 + - - +
46D LYS 3.0 4.0 + - - -
47D LEU* 3.3 36.9 + - + +
48D LYS* 3.0 28.6 + - + +
71D ILE* 3.9 30.1 - - + -
72D ALA 4.6 0.9 - - - +
73D ASP 3.5 1.6 + - - -
75D HIS 2.8 29.3 + - - +
77D PRO* 4.0 31.0 - - + -
80D LEU* 4.1 16.4 - - + -
82D MET* 4.4 5.8 - - + -
88D ILE* 4.6 3.6 - - + -
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Residues in contact with LYS 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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43D HIS* 3.1 7.0 - - + -
44D LEU* 1.3 78.9 - - - +
46D LYS* 1.3 58.1 + - - +
48D LYS* 3.8 6.1 - - - +
49D GLU* 2.9 49.8 + - + +
59D MET* 5.1 1.0 - - + +
73D ASP* 3.1 57.8 + - + +
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Residues in contact with LYS 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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42D THR* 6.3 1.1 - - + -
43D HIS 3.9 9.2 + - - +
44D LEU 3.0 0.6 - - - -
45D LYS* 1.3 76.7 - - - +
47D LEU* 1.3 56.0 + - - +
48D LYS 3.0 1.6 - - - -
49D GLU* 2.6 12.5 + - - +
50D SER* 2.6 37.1 + - - -
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Residues in contact with LEU 47 (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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24D LEU* 3.9 20.0 - - + -
26D VAL* 3.7 13.2 - - + -
36D PHE* 3.5 41.1 - - + -
38D VAL* 3.9 18.6 - - + -
44D LEU* 3.3 39.2 + - + +
46D LYS* 1.3 77.4 - - - +
48D LYS* 1.3 65.8 + - + +
50D SER* 3.4 6.9 + - - -
51D TYR* 3.0 24.8 + - - +
64D PHE* 4.8 6.7 - - + -
88D ILE* 4.1 10.8 - - + -
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Residues in contact with LYS 48 (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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44D LEU* 3.0 22.1 + - + +
45D LYS* 3.8 4.7 - - - +
46D LYS 3.0 0.4 - - - -
47D LEU* 1.3 82.7 - - + +
49D GLU* 1.3 61.8 + - - +
51D TYR* 3.4 2.8 + - - +
52D CYS* 3.1 28.1 + - - -
59D MET* 3.9 21.2 - - + +
64D PHE* 3.5 42.2 - - + -
70D ARG* 6.3 0.4 - - - +
71D ILE* 3.2 42.2 + - + +
72D ALA* 3.8 1.0 - - - +
73D ASP* 2.7 39.3 + - - +
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Residues in contact with GLU 49 (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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45D LYS* 2.9 58.4 + - + +
46D LYS* 2.6 14.8 + - - +
48D LYS* 1.3 70.4 - - - +
50D SER* 1.3 61.0 + - - +
52D CYS* 3.5 2.9 + - - +
53D GLN* 2.9 38.3 + - + +
59D MET* 3.8 25.9 - - + +
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Residues in contact with SER 50 (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 PHE* 3.4 22.6 - - - -
46D LYS 2.6 19.1 + - - -
47D LEU* 3.7 6.5 - - - -
49D GLU* 1.3 71.2 - - - +
51D TYR* 1.3 65.9 + - - +
53D GLN* 3.0 16.1 + - - +
54D ARG* 3.0 25.5 + - - +
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D VAL* 3.5 35.9 + - + -
28D GLY* 4.5 8.3 + - - -
32D SER* 4.3 11.3 + - - -
34D ILE* 3.4 32.5 - - + -
36D PHE* 4.0 12.0 - + + -
47D LEU 3.0 18.1 + - - +
48D LYS 3.5 4.9 - - - +
50D SER* 1.3 76.8 - - - +
52D CYS* 1.3 63.6 + - - +
54D ARG* 3.1 12.7 + - - +
55D GLN* 3.0 47.7 + - + +
62D LEU* 3.9 13.2 - - + -
64D PHE* 3.5 25.4 - + + -
90D VAL* 3.9 19.7 - - + +
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Residues in contact with CYS 52 (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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48D LYS 3.1 17.7 + - - +
49D GLU 3.9 4.7 - - - +
50D SER 3.3 0.2 - - - -
51D TYR* 1.3 79.9 - - - +
53D GLN* 1.3 53.3 + - + +
55D GLN* 3.1 3.3 + - - +
56D GLY 2.6 29.8 + - - -
57D VAL* 3.0 31.2 + - - +
58D PRO 4.1 2.5 - - - -
59D MET* 3.9 36.3 - - + +
62D LEU* 3.9 22.4 - - - -
64D PHE* 4.2 9.0 - - - -
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Residues in contact with GLN 53 (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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49D GLU* 2.9 28.2 + - - +
50D SER* 3.0 14.1 + - - +
52D CYS* 1.3 72.8 - - + +
54D ARG* 1.3 59.2 + - - +
55D GLN 2.8 4.5 - - - -
56D GLY* 2.8 21.7 + - - +
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Residues in contact with ARG 54 (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 ILE* 3.9 25.6 - - + -
36D PHE* 6.3 0.7 - - + -
50D SER* 3.0 15.2 + - - +
51D TYR* 3.1 8.0 + - - +
53D GLN* 1.3 75.2 + - - +
55D GLN* 1.3 64.3 + - - +
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Residues in contact with GLN 55 (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 SER* 4.8 5.7 + - - -
34D ILE* 3.9 9.9 - - - +
51D TYR* 3.0 55.2 + - + +
52D CYS* 3.1 7.6 + - - +
53D GLN 2.8 0.2 - - - -
54D ARG* 1.3 84.0 + - - +
56D GLY* 1.3 66.1 + - - +
57D VAL* 3.6 20.6 - - + +
62D LEU* 5.0 2.2 - - + -
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Residues in contact with GLY 56 (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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52D CYS 2.6 8.6 + - - -
53D GLN* 2.8 12.9 + - - -
55D GLN* 1.3 79.9 - - - +
57D VAL* 1.3 61.4 + - - +
58D PRO* 4.8 0.7 - - - +
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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