Contacts of the helix formed by residues 77 - 84 (chain B) in PDB entry 5TXN
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 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 3.7 26.5 - - + -
75B VAL* 3.2 29.8 + - + -
76B ASP* 1.3 72.2 - - - +
78B ARG* 1.3 55.1 + - - +
79B GLU 3.1 3.1 - - - -
80B LEU* 3.0 34.2 + - + +
81B ASN* 2.6 46.0 + - - +
128B THR* 4.3 25.8 - - + -
146B TYR* 4.7 2.7 - + - -
150B PRO* 3.7 24.2 - - + -
151B GLN 3.6 17.7 - - - -
152B GLY 3.6 17.5 - - - +
153B TRP* 3.5 22.2 - - + -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 5.2 2.6 - - - -
76B ASP* 2.7 39.1 + - - +
77B PHE* 1.3 76.0 - - - +
79B GLU* 1.3 62.2 + - - +
81B ASN* 3.9 9.5 - - - +
82B LYS* 3.1 32.2 + - - +
402B TRP* 4.3 7.1 - - - -
411B ILE* 3.2 39.9 - - + +
412B PRO 3.0 22.2 + - - -
413B GLU* 3.9 22.5 - - + +
414B TRP* 3.3 43.0 - - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 6.1 0.3 - - - +
19B PRO* 3.9 13.9 - - + -
20B LYS 5.2 0.2 - - - +
21B VAL* 4.0 25.4 - - + +
58B THR* 5.6 1.1 - - - +
76B ASP 4.7 2.9 + - - +
77B PHE 3.1 0.8 - - - -
78B ARG* 1.3 77.9 - - - +
80B LEU* 1.3 64.9 + - - +
82B LYS* 3.5 27.3 + - - +
83B ARG* 2.7 72.0 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.4 6.1 - - + -
19B PRO* 3.7 37.3 - - + +
58B THR* 4.6 1.0 + - - +
77B PHE* 3.0 41.3 + - + +
79B GLU* 1.3 78.4 - - - +
81B ASN* 1.3 62.6 + - - +
83B ARG* 3.0 12.6 + - + +
84B THR* 2.9 20.9 + - - +
124B PHE* 4.1 19.1 - - + -
127B TYR* 3.7 25.1 - - + +
128B THR* 4.5 4.7 - - + -
153B TRP* 3.6 28.3 - - + +
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 2.6 29.1 + - - +
78B ARG* 3.9 8.3 - - - +
80B LEU* 1.3 71.2 - - - +
82B LYS* 1.3 63.4 + - + +
84B THR* 3.1 4.3 + - - +
85B GLN* 3.0 19.2 + - - -
88B TRP* 3.4 14.7 + - - +
152B GLY 3.4 19.6 + - - -
153B TRP* 3.1 14.2 - - - -
154B LYS* 2.8 55.3 + - + +
184B MET* 4.5 2.2 - - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 3.3 10.6 - - - +
16B MET* 4.3 8.1 - - + +
78B ARG* 3.1 19.1 + - - +
79B GLU* 3.5 31.8 + - - +
80B LEU 3.3 0.2 - - - -
81B ASN* 1.3 77.0 - - + +
83B ARG* 1.3 59.0 + - + +
85B GLN* 3.2 33.0 - - - +
88B TRP* 5.3 1.1 - - - -
413B GLU* 3.3 35.2 + - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.4 18.9 - - + -
13B LYS* 2.7 34.1 + - - +
16B MET* 3.9 29.5 - - + +
17B ASP* 2.3 47.5 + - - +
18B GLY 3.9 6.6 + - - -
19B PRO* 3.8 17.7 - - - +
20B LYS 5.7 0.8 - - - +
79B GLU* 2.7 50.9 + - - +
80B LEU* 3.0 9.2 + - + +
82B LYS* 1.3 77.2 - - + +
84B THR* 1.3 53.9 + - - +
85B GLN 3.4 0.2 - - - -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.1 16.8 - - + -
11B LYS 3.8 14.6 - - - +
12B LEU* 4.1 3.6 - - - +
13B LYS* 4.1 3.6 - - - +
80B LEU* 2.9 16.0 + - - +
81B ASN 3.1 6.0 + - - -
83B ARG* 1.3 77.1 - - - +
85B GLN* 1.3 63.7 + - - +
86B ASP 3.3 2.5 - - - -
87B PHE* 2.9 37.8 + - + -
88B TRP* 3.0 14.1 + - + -
124B PHE* 4.0 11.2 - - + -
153B TRP* 3.8 22.8 + - + +
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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