Contacts of the helix formed by residues 39 - 51 (chain D) in PDB entry 2IY1
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.7 2.9 - - + -
33D VAL* 4.8 6.3 - - + -
37D THR 4.9 0.7 - - - +
38D HIS* 1.3 72.5 - - - +
40D LYS* 1.3 63.2 + - - +
41D LYS 3.4 0.9 - - - -
42D LEU* 3.3 36.5 + - + +
43D LYS* 3.0 27.1 + - + +
66D ILE* 3.7 35.0 - - + -
67D ALA 4.5 1.8 - - - +
68D ASP 3.6 2.2 + - - -
70D HIS 2.9 21.5 + - - +
72D PRO* 3.9 31.2 - - + -
75D LEU* 3.8 21.1 - - + -
77D MET* 4.0 5.2 - - + -
83D ILE* 4.6 9.0 - - + -
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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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38D HIS* 3.2 6.4 - - + -
39D LEU* 1.3 75.8 - - - +
41D LYS* 1.3 63.9 + - - +
43D LYS* 3.0 7.8 + - - +
44D GLU* 2.9 54.9 + - + +
68D ASP* 3.3 54.3 + - + +
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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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37D THR* 6.0 4.3 - - + -
38D HIS 4.1 6.7 + - - +
39D LEU 3.4 0.6 - - - -
40D LYS* 1.3 77.8 - - - +
42D LEU* 1.3 56.3 + - - +
44D GLU* 3.8 14.4 - - + +
45D SER* 2.9 41.6 + - - +
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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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19D LEU* 4.2 16.8 - - + -
21D VAL* 4.0 20.2 - - + -
31D PHE* 3.9 40.6 - - + -
33D VAL* 4.6 14.6 - - + +
38D HIS 4.9 1.2 + - - +
39D LEU* 3.3 34.4 + - + +
40D LYS 3.3 0.6 - - - -
41D LYS* 1.3 78.8 - - - +
43D LYS* 1.3 71.8 + - + +
45D SER* 3.3 6.2 + - - -
46D TYR* 3.0 20.8 + - + +
59D PHE* 4.9 8.7 - - + -
83D ILE* 4.3 13.0 - - + -
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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 LEU* 3.0 23.6 + - + +
40D LYS 3.0 6.8 + - - +
42D LEU* 1.3 78.3 - - + +
44D GLU* 1.3 62.7 + - - +
46D TYR* 3.2 4.0 + - - +
47D CYS* 3.1 23.6 + - - -
54D MET* 3.5 18.6 - - + -
59D PHE* 3.4 48.6 - - + -
65D ARG* 6.2 0.4 - - - +
66D ILE* 2.9 39.6 + - + +
67D ALA* 3.2 0.8 - - - +
68D ASP* 2.9 44.3 + - - +
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Residues in contact with GLU 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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40D LYS* 2.9 56.2 + - - +
41D LYS* 3.9 14.9 - - + +
43D LYS* 1.3 71.8 - - - +
45D SER* 1.3 61.0 + - - +
47D CYS* 3.2 10.3 - - - -
48D GLN* 3.0 30.5 + - - +
54D MET* 3.6 21.2 - - + +
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Residues in contact with SER 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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31D PHE* 4.0 20.4 - - - -
41D LYS* 2.9 31.1 + - - +
42D LEU* 3.4 5.1 - - - -
44D GLU* 1.3 74.0 - - - +
46D TYR* 1.3 55.8 + - - +
48D GLN* 3.2 6.0 + - - +
49D ARG* 2.8 36.9 + - - +
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Residues in contact with TYR 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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21D VAL* 3.3 38.8 - - + -
23D GLY* 3.7 24.8 + - - -
27D SER* 4.4 7.8 + - - -
29D ILE* 3.7 24.5 - - + +
31D PHE* 4.2 13.4 - + + -
42D LEU* 3.0 14.2 + - + +
43D LYS 3.2 8.0 + - - +
45D SER* 1.3 75.4 - - - +
47D CYS* 1.3 60.4 + - - +
49D ARG* 3.1 10.3 + - - +
50D GLN* 2.9 56.1 + - + +
57D LEU* 4.1 6.3 - - + -
59D PHE* 3.9 22.9 - + + -
85D VAL* 3.8 22.2 - - + +
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Residues in contact with CYS 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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43D LYS 3.1 12.7 + - - +
44D GLU* 3.2 22.2 - - - -
46D TYR* 1.3 76.4 - - - +
48D GLN* 1.3 78.9 + - - +
50D GLN* 3.2 4.2 + - - -
51D GLY* 3.0 18.2 + - - -
52D VAL* 3.1 27.6 + - + +
54D MET* 4.1 27.1 - - - -
57D LEU* 3.7 28.3 - - + -
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Residues in contact with GLN 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 GLU 3.0 17.6 + - - +
45D SER* 3.4 7.0 - - - +
47D CYS* 1.3 81.3 - - - +
49D ARG* 1.3 67.7 + - - +
51D GLY* 3.0 15.5 + - - -
52D VAL 5.0 1.1 - - - -
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Residues in contact with ARG 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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29D ILE* 3.8 41.0 - - + +
31D PHE* 5.7 2.5 - - + -
45D SER 2.8 14.8 + - - +
46D TYR* 3.2 13.9 - - - +
48D GLN* 1.3 82.5 + - - +
50D GLN* 1.3 56.4 + - - +
51D GLY 3.6 0.2 + - - -
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Residues in contact with GLN 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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25D ASP* 5.2 4.6 + - - -
27D SER* 5.0 8.9 + - - -
29D ILE* 4.4 8.5 - - - +
46D TYR* 2.9 49.8 + - + +
47D CYS* 3.7 10.5 - - - +
48D GLN 3.2 0.2 - - - -
49D ARG* 1.3 76.5 - - - +
51D GLY* 1.3 61.2 + - - +
52D VAL* 3.3 22.2 + - + +
57D LEU* 5.5 1.3 - - + -
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Residues in contact with GLY 51 (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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47D CYS 3.0 3.6 + - - -
48D GLN* 3.0 13.4 + - - -
49D ARG 3.3 1.2 + - - -
50D GLN* 1.3 77.6 - - - +
52D VAL* 1.3 61.2 + - - +
53D PRO* 4.9 0.3 - - - +
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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