Contacts of the helix formed by residues 52 - 64 (chain D) in PDB entry 5W97
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 SER 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D SER 3.7 1.8 + - - -
51D LEU* 1.3 76.3 - - - +
53D ILE* 1.3 62.2 + - - +
54D ASP* 4.0 8.1 + - - +
55D GLU* 3.0 37.4 + - - +
56D LYS* 3.0 29.6 + - - +
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Residues in contact with ILE 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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51D LEU 5.7 0.4 - - - +
52D SER* 1.3 74.5 - - - +
54D ASP* 1.3 66.0 + - - +
56D LYS* 3.3 8.3 + - + +
57D VAL* 2.9 34.5 + - + +
99E SER* 4.0 21.3 - - - +
103E GLU* 4.4 17.7 - - + +
104E LEU* 4.0 20.0 - - + +
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Residues in contact with ASP 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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52D SER* 3.3 9.1 + - - +
53D ILE* 1.3 85.1 - - - +
55D GLU* 1.3 59.1 + - + +
57D VAL* 3.5 8.0 + - - +
58D GLU* 3.0 26.0 + - - +
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Residues in contact with GLU 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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40D LEU* 3.6 24.8 - - + +
43D LYS* 2.8 42.0 + - - +
51D LEU* 3.5 7.0 - - + -
52D SER* 3.0 40.2 + - - +
53D ILE 3.2 0.6 - - - -
54D ASP* 1.3 75.7 - - + +
56D LYS* 1.3 60.7 + - - +
58D GLU* 3.2 9.2 + - - +
59D LEU* 3.0 34.0 + - - +
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Residues in contact with LYS 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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48D TRP 3.1 24.2 + - - -
49D SER* 4.9 1.6 - - - +
51D LEU* 3.9 23.7 + - + +
52D SER 3.0 19.3 + - - +
53D ILE* 3.5 8.6 - - + +
55D GLU* 1.3 72.7 - - - +
57D VAL* 1.3 64.5 + - - +
59D LEU* 3.3 3.8 + - - +
60D TYR* 3.0 19.6 + - - +
61E PHE* 3.4 41.1 - - + -
97E GLY* 2.4 31.7 + - - -
99E SER* 3.1 28.5 + - - +
104E LEU* 3.8 11.7 - - + -
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Residues in contact with VAL 57 (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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53D ILE* 2.9 26.1 + - + +
54D ASP* 3.9 8.3 - - - +
56D LYS* 1.3 73.4 - - - +
58D GLU* 1.3 63.3 + - - +
60D TYR* 3.1 8.3 + - - +
61D ARG* 3.0 39.2 + - + +
104E LEU* 3.5 38.4 - - + +
106E LEU* 4.8 10.8 - - + -
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Residues in contact with GLU 58 (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 GLN* 3.9 24.9 - - - +
40D LEU* 3.5 24.0 - - + +
54D ASP 3.0 17.3 + - - +
55D GLU* 3.5 8.6 - - - +
56D LYS 3.2 0.6 - - - -
57D VAL* 1.3 78.7 - - - +
59D LEU* 1.3 57.8 + - - +
61D ARG* 3.2 8.4 + - + +
62D LEU* 3.0 33.1 + - + +
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Residues in contact with LEU 59 (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 LEU* 3.7 33.2 - - + +
41D LYS* 3.9 29.5 + - + +
44D GLU* 3.8 37.2 - - + +
51D LEU* 3.9 23.3 - - + -
55D GLU 3.0 19.3 + - - +
56D LYS 3.7 4.3 - - - +
57D VAL 3.3 0.2 - - - -
58D GLU* 1.3 72.7 - - - +
60D TYR* 1.3 68.0 + - - +
62D LEU* 3.2 15.3 + - + +
63D LYS* 3.3 8.0 + - - +
61E PHE* 4.3 15.3 - - + -
62E ALA* 3.6 10.4 - - + +
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Residues in contact with TYR 60 (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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56D LYS 3.0 13.0 + - - +
57D VAL 3.1 8.9 + - - +
59D LEU* 1.3 74.7 - - - +
61D ARG* 1.3 66.7 + - - +
63D LYS* 3.1 7.4 + - - +
64D PHE* 3.0 60.5 + + + -
67D SER* 3.5 19.4 - - - -
61E PHE* 5.5 1.8 - - + -
62E ALA* 3.8 22.3 - - + +
65E VAL* 4.0 13.9 - - + -
66E ARG* 2.8 21.7 + - - -
69E GLU* 2.5 36.7 + - - -
104E LEU* 5.6 0.4 - - + -
106E LEU* 3.5 39.7 - - + -
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Residues in contact with ARG 61 (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 HIS* 3.3 23.6 - - - -
30D VAL* 3.9 3.1 - - - +
57D VAL* 3.0 28.3 + - + +
58D GLU* 3.2 10.7 + - + +
60D TYR* 1.3 80.7 - - + +
62D LEU* 1.3 62.6 + - - +
63D LYS 3.4 0.2 - - - -
64D PHE 3.6 5.2 - - - -
65D LYS 2.9 28.9 + - - -
66D GLU 4.1 0.2 - - - -
67D SER* 3.8 8.7 + - - +
70D GLU* 2.9 38.1 + - - -
106E LEU* 3.7 28.1 - - - +
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Residues in contact with LEU 62 (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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28D ALA* 4.2 1.3 - - - +
29D HIS* 3.5 0.5 + - - +
30D VAL* 2.8 61.5 + - + +
33D LEU* 3.9 18.2 - - + -
37D GLN* 3.7 39.3 - - + +
40D LEU* 4.4 16.4 - - + -
41D LYS* 4.3 23.8 - - + +
58D GLU* 3.0 21.9 + - + +
59D LEU* 3.2 9.6 + - - +
61D ARG* 1.3 77.9 - - - +
63D LYS* 1.3 60.2 + - - +
64D PHE 3.6 0.2 - - - -
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Residues in contact with LYS 63 (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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16D TYR* 3.6 7.6 - - - -
25D PRO* 5.4 0.2 - - - +
27D VAL 4.4 1.5 - - - +
28D ALA* 3.7 20.3 - - + +
29D HIS 2.9 19.8 + - - +
41D LYS* 5.6 9.0 - - - +
59D LEU 3.3 1.7 + - - +
60D TYR 3.1 9.7 + - - +
62D LEU* 1.3 80.8 - - - +
64D PHE* 1.3 84.1 + - + +
26E ALA* 6.2 1.2 - - - +
30E ARG* 5.5 11.1 - - - +
60E ASP* 3.1 40.3 + - - -
62E ALA* 3.6 16.4 - - + -
63E SER* 3.7 6.4 + - - -
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Residues in contact with PHE 64 (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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16D TYR* 3.2 10.8 - + - +
23D PRO 3.8 8.5 - - - -
24D LEU* 3.9 11.0 - - + -
25D PRO* 4.0 13.7 - - + -
29D HIS* 3.6 6.2 - - - -
60D TYR* 3.0 38.3 + + + +
61D ARG* 3.3 26.9 + - - +
62D LEU 3.6 0.2 - - - -
63D LYS* 1.3 101.4 - - + +
65D LYS* 1.3 64.4 + - - +
66D GLU 4.4 1.1 - - - +
62E ALA 3.4 25.6 - - - -
63E SER* 4.1 4.5 - - - -
66E ARG* 3.5 57.0 - - + +
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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