Contacts of the helix formed by residues 85 - 97 (chain A) in PDB entry 3DRB
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 PHE 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.8 31.2 - - + -
45A LYS* 3.9 12.1 - - + -
47A THR* 4.1 8.1 - - + -
51A PHE 3.5 20.9 - - - -
52A THR* 3.6 10.3 - - - -
53A LEU* 3.5 39.0 - - + -
56A VAL* 3.8 20.6 - - + -
81A SER* 2.9 21.4 + - - +
84A VAL* 1.3 100.3 - - + +
86A LYS* 1.3 58.1 + - - +
87A ASP 3.1 3.8 - - - +
88A LEU* 2.9 25.9 + - + +
89A PHE* 3.0 25.1 + - + -
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR 3.3 21.4 + - - +
83A GLU* 3.2 32.0 + - - +
84A VAL 3.4 1.7 - - - +
85A PHE* 1.3 76.8 - - - +
87A ASP* 1.3 74.4 + - - +
88A LEU 3.0 0.2 - - - -
89A PHE* 4.4 2.7 - - - +
90A ASP* 2.8 67.7 + - - +
102A PRO* 5.3 5.1 - - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 5.5 0.2 - - - +
38A LEU* 3.7 32.7 - - + +
41A GLU* 5.5 1.6 - - - +
42A LEU* 4.2 17.2 - - + +
45A LYS* 5.9 0.7 - - - -
84A VAL 5.1 0.8 + - - -
85A PHE 3.1 0.8 - - - -
86A LYS* 1.3 92.8 + - - +
88A LEU* 1.3 56.3 + - - +
90A ASP* 5.1 1.2 - - - +
91A PRO* 3.4 19.7 - - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 4.6 4.9 - - + -
33A VAL* 3.4 29.2 - - + +
34A LEU* 4.3 18.8 - - + -
38A LEU* 4.1 13.2 - - + -
42A LEU* 4.4 13.3 - - + +
53A LEU* 3.9 8.1 - - + -
56A VAL* 3.6 31.4 - - + -
57A ILE* 3.9 14.6 - - + -
74A CYS* 4.6 4.9 - - + -
85A PHE* 2.9 11.6 + - + +
87A ASP* 1.3 79.1 - - - +
89A PHE* 1.3 69.0 + - + +
91A PRO* 3.2 10.4 - - - +
92A ILE* 3.3 30.0 + - + +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 3.7 13.9 - - + -
74A CYS* 3.9 19.5 - - - -
75A VAL 3.7 28.0 - - - -
76A ALA* 4.1 7.2 - - + -
81A SER* 3.3 31.9 - - - -
82A TYR* 3.7 29.4 - + + +
85A PHE* 3.0 30.9 + - + +
86A LYS* 4.4 4.3 - - - +
88A LEU* 1.3 81.4 - - + +
90A ASP* 1.3 55.2 + - - +
92A ILE* 3.1 5.5 + - + +
93A ILE* 2.7 45.3 + - + +
284A PRO* 3.8 30.5 - - + -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR 5.1 0.9 - - - +
86A LYS* 2.8 65.9 + - - +
87A ASP* 5.1 1.3 - - - +
89A PHE* 1.3 73.2 - - - +
91A PRO* 1.3 61.5 - - + +
93A ILE* 3.3 11.6 + - - +
94A GLU* 2.9 30.1 + - - +
100A TYR 4.8 0.7 - - - +
102A PRO* 4.0 30.7 - - + +
276A HIS* 4.4 15.4 + - - -
277A LEU* 5.8 0.9 - - - +
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.8 25.3 - - + +
87A ASP* 3.4 20.9 - - - +
88A LEU 3.2 12.8 - - - +
90A ASP* 1.3 96.2 - - + +
92A ILE* 1.3 56.1 + - - +
94A GLU* 3.3 10.5 + - + +
95A ASP* 2.9 31.2 + - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.0 27.6 + - + +
30A MET* 3.9 18.8 - - - -
33A VAL* 3.8 15.3 - - + -
72A VAL* 4.1 18.4 - - + -
74A CYS* 3.4 26.5 - - - -
88A LEU* 3.3 30.5 + - + +
89A PHE* 3.1 9.3 + - - +
91A PRO* 1.3 78.1 - - - +
93A ILE* 1.3 57.6 + - - +
95A ASP* 3.8 4.0 - - - +
96A ARG* 2.9 32.2 + - + +
284A PRO* 4.4 12.6 - - + -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 4.5 5.4 - - + -
89A PHE* 2.7 38.0 + - + +
90A ASP* 3.7 11.7 - - - +
92A ILE* 1.3 70.8 - - - +
94A GLU* 1.3 59.6 + - - +
96A ARG* 4.6 0.7 - - - -
97A HIS* 2.9 38.2 + - + +
100A TYR* 4.1 15.7 - - + +
276A HIS* 5.6 1.8 - - - +
277A LEU* 4.1 18.8 - - + -
284A PRO* 4.3 13.0 - - + -
287A LEU* 3.7 27.8 - - + -
342A LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP 2.9 16.7 + - - +
91A PRO* 3.6 9.9 - - + +
93A ILE* 1.3 80.3 - - - +
95A ASP* 1.3 61.2 + - - +
98A GLY 3.5 1.9 + - - -
99A GLY* 2.7 43.4 + - - -
100A TYR 3.2 23.6 - - - +
101A LYS* 2.6 41.3 + - - +
102A PRO* 4.1 12.1 - - + +
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.9 22.2 - - - +
32A LYS* 2.8 38.8 + - + +
33A VAL* 5.9 3.0 - - + +
70A MET* 4.8 2.1 - - - +
91A PRO 2.9 17.5 + - - +
92A ILE* 3.8 3.6 - - - +
94A GLU* 1.3 78.8 - - - +
96A ARG* 1.3 62.0 + - - +
98A GLY* 3.7 7.8 + - - -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.9 30.0 - - + +
70A MET 5.8 1.5 + - - -
72A VAL* 4.7 7.7 - - + +
92A ILE* 2.9 23.3 + - + +
93A ILE* 4.1 2.0 - - - +
95A ASP* 1.3 79.5 - - - +
97A HIS* 1.3 83.4 + - + +
98A GLY 3.4 2.6 + - - -
284A PRO* 5.2 1.3 - - + +
285A SER* 3.6 36.8 + - - +
339A ALA 5.4 5.9 + - - -
341A ARG* 5.7 4.4 - - - +
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 2.9 34.4 + - + +
94A GLU 3.8 0.7 - - - -
96A ARG* 1.3 90.6 + - + +
98A GLY* 1.3 64.0 + - - +
99A GLY 3.4 2.9 + - - -
100A TYR* 3.5 20.8 + - + +
284A PRO 2.9 24.3 + - - -
285A SER* 3.3 28.6 - - - -
287A LEU* 4.6 2.4 - - - +
341A ARG* 4.0 16.3 + - + +
342A LEU* 3.8 44.6 + - + +
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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