Contacts of the helix formed by residues 75 - 84 (chain D) in PDB entry 5TBY
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 GLN 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801B TYR* 3.8 14.0 + - + +
804B LEU* 2.6 36.9 - - - +
61D PHE* 4.2 16.5 - - + +
63D ARG* 2.7 30.2 + - - +
70D LYS 5.1 0.5 - - - +
71D ILE* 4.2 9.4 - - + +
72D THR* 2.9 45.7 + - - +
74D GLY* 1.3 70.7 - - - +
76D CYS* 1.3 60.4 + - - +
77D GLY* 3.0 6.8 + - - -
78D ASP* 3.5 6.7 + - - +
79D VAL* 3.2 24.3 + - - +
104D LEU* 5.3 3.3 - - + +
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Residues in contact with CYS 76 (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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71D ILE* 4.9 7.2 - - + -
72D THR 3.3 8.7 + - - +
73D TYR* 3.2 22.9 - - - +
75D GLN* 1.3 75.6 - - - +
77D GLY* 1.3 61.1 + - - +
79D VAL* 2.9 25.9 - - - +
80D LEU* 3.2 29.4 - - - +
92D VAL* 4.0 12.1 - - + -
95D VAL* 4.4 16.8 - - - -
96D LEU* 6.2 1.8 - - + -
109D MET* 6.4 1.3 - - + -
114D PHE* 5.3 7.9 - - - -
117D MET* 5.5 6.5 - - - -
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Residues in contact with GLY 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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74D GLY 3.1 10.9 + - - -
75D GLN 3.0 3.4 - - - -
76D CYS* 1.3 81.2 - - - +
78D ASP* 1.3 63.6 + - - -
79D VAL 3.3 0.3 + - - -
80D LEU* 3.4 3.8 + - - +
81D ARG* 3.3 30.5 + - - +
87D PRO* 4.7 1.7 - - - +
92D VAL* 3.8 24.4 - - - +
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Residues in contact with ASP 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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797B ALA* 3.2 23.7 - - + +
801B TYR* 3.7 36.3 - - + -
61D PHE* 4.4 2.8 - - - -
74D GLY 5.3 2.4 - - - +
75D GLN* 3.5 5.5 + - - +
77D GLY* 1.3 72.0 - - - +
79D VAL* 1.3 59.4 + - - +
81D ARG* 2.9 33.7 + - + +
82D ALA* 2.9 31.0 + - - +
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Residues in contact with VAL 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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57D ALA* 4.8 6.7 - - + +
58D PHE* 5.3 1.6 - - + +
61D PHE* 3.0 41.3 - - + -
71D ILE* 4.7 6.7 - - + -
75D GLN 3.2 6.7 + - - +
76D CYS* 2.9 42.2 - - - +
78D ASP* 1.3 76.1 - - - +
80D LEU* 1.3 55.2 - - + +
82D ALA* 3.1 6.8 + - - +
83D LEU* 2.9 40.0 + - + +
114D PHE* 3.5 40.4 - - + -
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Residues in contact with LEU 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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76D CYS* 3.2 31.6 - - - +
77D GLY 3.4 6.2 + - - +
79D VAL* 1.3 82.0 - - + +
81D ARG* 1.3 62.8 + - - +
83D LEU* 3.0 18.6 + - + +
84D GLY 3.1 9.2 + - - -
85D GLN* 3.3 17.3 + - + +
87D PRO* 4.4 18.8 - - + -
91D GLU 6.0 0.2 - - - -
92D VAL* 4.9 7.6 - - + -
95D VAL* 5.0 4.7 - - + -
114D PHE* 4.1 9.0 - - + -
117D MET* 5.5 2.0 - - + -
118D LEU* 3.1 35.2 - - + +
121D ILE* 4.3 33.7 - - + -
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Residues in contact with ARG 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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793B ARG* 3.8 36.8 + - - +
794B GLY* 5.3 7.9 - - - +
797B ALA* 4.5 14.3 - - + +
798B ARG* 3.9 9.7 + - - -
77D GLY* 3.3 15.5 + - - +
78D ASP* 2.9 47.9 + - + +
79D VAL 3.1 0.4 - - - -
80D LEU* 1.3 76.6 - - - +
82D ALA* 1.3 57.7 + - - +
84D GLY* 2.9 23.2 + - - -
85D GLN 3.5 8.2 + - - -
86D ASN* 5.1 7.2 + - - +
87D PRO* 4.0 29.9 + - + +
88D THR 5.7 0.2 - - - -
89D GLN* 4.5 10.7 - - - +
92D VAL* 5.9 2.2 - - - +
162D GLU* 3.4 26.3 + - - -
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Residues in contact with ALA 82 (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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797B ALA* 6.1 1.8 - - - +
798B ARG* 4.4 24.0 + - - +
53D GLU* 5.2 1.6 - - - +
57D ALA* 5.4 4.7 - - + -
61D PHE* 4.6 13.5 - - + -
78D ASP 2.9 13.8 + - - +
79D VAL 3.4 8.3 - - - +
81D ARG* 1.3 75.5 - - - +
83D LEU* 1.3 63.7 + - + +
84D GLY* 3.3 1.9 + - - -
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Residues in contact with LEU 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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53D GLU* 3.5 51.4 - - + +
54D PHE* 3.4 31.5 - - + -
57D ALA* 3.8 15.9 - - + -
79D VAL* 2.9 18.5 + - + +
80D LEU* 3.0 15.2 + - + +
82D ALA* 1.3 76.2 - - - +
84D GLY* 1.3 56.7 + - - +
85D GLN* 3.5 8.4 + - + +
114D PHE* 3.5 17.5 - - + -
118D LEU* 3.3 33.2 - - + -
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Residues in contact with GLY 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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798B ARG* 4.1 15.6 + - - -
80D LEU 3.1 0.4 + - - -
81D ARG 2.9 13.8 + - - -
82D ALA 3.1 0.8 - - - -
83D LEU* 1.3 78.4 - - - +
85D GLN* 1.3 68.4 + - - +
86D ASN* 3.5 15.4 + - - +
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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