Contacts of the helix formed by residues 74 - 89 (chain D) in PDB entry 1DS5
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 LYS 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A VAL 5.4 3.0 + - - -
205A ASP* 5.3 10.9 - - - +
263A ILE* 5.5 0.4 - - - +
264A GLU* 3.1 46.9 + - + +
265A LEU 4.6 2.5 - - - +
266A ASP* 3.7 31.4 + - - -
267A PRO* 4.4 3.8 - - + +
73D VAL* 1.3 74.5 - - - +
75D LYS* 1.3 59.0 + - - +
76D LYS* 3.5 35.3 - - + +
77D LYS* 2.6 38.4 + - + +
78D ILE* 3.4 3.8 + - - +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 2.4 43.4 + - - +
265A LEU 5.7 2.0 + - - +
73D VAL 3.2 5.6 + - - +
74D LYS* 1.3 71.3 - - - +
76D LYS* 1.3 56.3 + - - +
78D ILE* 2.9 27.3 + - - +
79D LYS* 2.9 28.8 + - + +
102D ARG* 6.1 2.5 - - - +
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Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG 4.1 10.1 + - - +
263A ILE* 4.2 11.3 - - - +
264A GLU* 2.9 43.2 + - + +
26D TYR* 3.4 18.3 - - + -
27D GLU* 3.6 35.7 - - + +
74D LYS* 2.8 38.3 + - + +
75D LYS* 1.3 76.0 - - - +
77D LYS* 1.3 63.3 + - + +
78D ILE 3.0 1.0 + - - -
79D LYS* 3.9 11.0 - - + +
80D ARG* 3.3 14.7 + - - +
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Residues in contact with LYS 77 (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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50D TYR* 3.8 42.5 - - - +
73D VAL* 4.8 16.8 - - + +
74D LYS* 2.6 27.9 + - + +
76D LYS* 1.3 76.6 - - + +
78D ILE* 1.3 59.8 + - + +
80D ARG* 3.9 29.0 + - - +
81D GLU* 3.9 21.4 + - - +
177D GLY* 3.2 35.1 + - - +
178D LEU* 5.0 3.4 - - - -
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Residues in contact with ILE 78 (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 VAL* 5.6 2.0 - - + -
33D TRP* 6.2 3.1 - - + -
70D LEU* 3.2 37.0 - - + -
71D LYS 4.9 0.4 - - - +
73D VAL* 3.8 31.2 - - + +
74D LYS 3.9 6.1 - - - +
75D LYS* 2.9 11.2 + - - +
77D LYS* 1.3 83.6 - - + +
79D LYS* 1.3 70.3 + - + +
80D ARG 2.8 2.3 + - - -
81D GLU* 3.4 4.7 + - + +
82D ILE* 3.0 44.8 + - + +
109D PRO* 3.8 22.4 - - + -
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Residues in contact with LYS 79 (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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26D TYR* 3.4 16.8 - - - +
27D GLU* 3.6 22.4 - - + +
29D LEU* 3.0 43.4 + - + +
30D THR* 4.8 3.6 - - - +
31D VAL* 4.7 15.4 - - + +
33D TRP* 6.2 1.0 - - - -
75D LYS* 2.9 28.9 + - + +
76D LYS* 3.7 6.9 + - - +
78D ILE* 1.3 79.4 - - + +
80D ARG* 1.3 55.8 + - - +
82D ILE* 3.7 6.6 - - - +
83D LYS* 2.8 33.3 + - - +
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Residues in contact with ARG 80 (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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26D TYR* 3.7 41.0 + - + -
76D LYS 3.3 17.4 + - - +
77D LYS* 3.9 28.8 + - - +
78D ILE 2.8 1.0 - - - -
79D LYS* 1.3 73.4 - - - +
81D GLU* 1.4 70.9 + - - +
83D LYS* 2.9 4.7 + - - +
84D ILE* 2.8 34.0 + - + +
155D ARG* 4.0 15.9 - - - +
176D TRP 5.1 0.4 + - - -
177D GLY 3.6 22.0 + - - -
178D LEU* 4.1 6.7 + - - +
179D ALA 2.9 25.2 + - - +
180D GLU* 3.6 25.1 + - - +
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Residues in contact with GLU 81 (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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68D LYS* 2.5 37.1 + - - +
70D LEU* 4.2 10.0 - - + +
77D LYS* 3.9 17.0 + - - +
78D ILE* 3.4 7.3 + - - +
80D ARG* 1.4 77.9 - - - +
82D ILE* 1.4 52.6 + - - +
84D ILE* 3.3 3.6 - - - +
85D LEU* 2.8 49.1 + - + +
111D LEU* 3.9 20.5 - - + +
113D PHE* 4.9 2.1 - - - -
175D ASP* 4.1 0.5 - - - -
176D TRP 3.2 23.4 + - - +
177D GLY* 3.0 33.4 + - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 4.4 11.4 - - + -
31D VAL* 3.4 26.0 - - + -
33D TRP* 5.8 0.2 - - + -
78D ILE* 3.0 38.7 + - + +
79D LYS* 3.7 5.6 - - - +
80D ARG 3.0 0.6 + - - -
81D GLU* 1.4 71.6 - - - +
83D LYS* 1.4 55.5 + - - +
85D LEU* 3.2 8.8 + - - +
86D GLN* 2.7 62.0 + - + +
97D LEU* 4.4 4.7 - - + +
100D ILE* 3.8 22.9 - - + -
111D LEU* 3.8 29.4 - - + -
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Residues in contact with LYS 83 (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 GLU* 2.6 33.3 + - - +
23D TYR* 3.1 19.8 + - - +
26D TYR* 3.7 25.6 - - + -
29D LEU* 4.2 17.3 - - + -
79D LYS 2.8 22.7 + - - +
80D ARG 2.9 3.6 + - - +
82D ILE* 1.4 72.7 - - - +
84D ILE* 1.3 51.4 + - - +
86D GLN* 2.9 25.7 + - - +
87D ASN* 2.6 61.9 + - - +
181D PHE* 4.3 2.5 - - + -
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Residues in contact with ILE 84 (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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80D ARG* 2.8 32.9 + - + +
81D GLU* 3.3 8.7 - - - +
83D LYS* 1.3 70.0 - - - +
85D LEU* 1.3 53.7 + - - +
87D ASN* 3.0 4.5 + - - +
88D LEU* 2.6 51.9 + - + +
152D ILE* 3.0 46.9 - - + -
176D TRP* 3.9 19.7 - - + -
179D ALA* 4.3 7.4 - - + +
180D GLU* 4.2 11.0 - - - -
181D PHE* 3.7 23.8 - - + -
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Residues in contact with LEU 85 (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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81D GLU* 2.8 43.4 + - + +
82D ILE 3.4 4.3 - - - +
84D ILE* 1.3 72.8 - - - +
86D GLN* 1.3 64.0 + - - +
88D LEU* 3.1 4.0 + - + +
89D CYS* 2.9 24.7 + - - +
94D ILE* 5.3 2.4 - - + +
95D VAL* 4.1 14.6 - - + +
97D LEU* 3.9 27.6 + - + +
111D LEU* 4.3 4.0 - - + -
113D PHE* 3.5 39.0 - - + -
176D TRP* 3.3 36.3 - - + +
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Residues in contact with GLN 86 (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 LEU* 3.9 13.5 - - - +
32D GLN* 6.1 1.6 - - - +
82D ILE* 2.7 39.0 + - + +
83D LYS* 3.4 27.8 - - + +
85D LEU* 1.3 71.9 - - - +
87D ASN* 1.3 63.9 + - - +
88D LEU 3.2 0.9 + - - -
89D CYS* 3.4 18.3 + - - +
97D LEU* 4.6 10.3 - - + +
100D ILE* 4.9 8.7 - - - +
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Residues in contact with ASN 87 (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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23D TYR* 3.0 47.1 + - - +
83D LYS* 2.6 38.5 + - - +
84D ILE* 3.2 10.2 - - - +
86D GLN* 1.3 75.1 - - - +
88D LEU* 1.3 63.4 + - - +
89D CYS 4.5 1.2 - - - +
146D TYR* 3.8 9.0 + - - -
150D GLN* 4.5 6.9 - - - +
152D ILE* 4.2 4.3 - - + -
181D PHE* 3.1 36.2 - - - -
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Residues in contact with LEU 88 (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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84D ILE* 2.6 32.4 + - + +
85D LEU* 4.0 3.4 - - - +
87D ASN* 1.3 74.9 - - - +
89D CYS* 1.4 55.5 + - - +
91D GLY* 2.5 37.6 + - - -
94D ILE* 3.8 17.3 - - + -
146D TYR* 3.3 19.1 + - + -
147D CYS* 3.6 25.1 - - + -
150D GLN* 4.0 15.3 - - + -
152D ILE* 4.1 9.9 - - + -
176D TRP* 3.3 50.3 - - + -
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Residues in contact with CYS 89 (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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85D LEU 2.9 16.9 + - - +
86D GLN* 3.4 18.5 + - - +
87D ASN 4.5 1.7 - - - +
88D LEU* 1.4 74.1 - - - +
90D GLY* 1.3 59.3 + - - +
91D GLY 3.5 0.3 + - - -
94D ILE* 4.8 4.9 - - - +
95D VAL 5.3 3.8 - - - -
96D LYS* 2.6 39.5 - - - +
97D LEU* 4.2 18.8 - - + +
98D LEU* 5.9 0.2 - - - -
146D TYR* 4.6 2.1 + - - -
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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