Contacts of the helix formed by residues 82 - 93 (chain f) in PDB entry 6A5T
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 THR 82 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85e GLN* 3.3 14.8 - - - +
88e ALA* 4.4 0.4 - - - -
76f ALA* 5.6 0.4 - - + -
78f ARG* 3.7 34.3 - - - +
80f THR 4.1 4.5 - - - +
81f VAL* 1.3 77.5 - - - +
83f ALA* 1.3 62.5 + - - +
84f MET* 3.1 15.3 + - + +
85f ASP* 2.5 49.4 + - - +
86f VAL* 3.2 22.5 + - - +
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Residues in contact with ALA 83 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85e GLN* 2.5 19.3 + - - +
87e ALA* 4.6 9.2 - - + -
88e ALA* 3.7 30.7 - - + +
91e ALA* 5.7 2.7 - - + -
82f THR* 1.3 71.6 - - - +
84f MET* 1.3 65.7 + - + +
86f VAL* 3.2 4.9 + - - +
87f VAL* 3.0 29.4 + - + +
100f PHE* 5.2 12.3 - - + +
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Residues in contact with MET 84 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82f THR* 3.1 12.3 + - - +
83f ALA* 1.3 80.6 - - + +
85f ASP* 1.3 57.1 + - - +
87f VAL* 3.0 7.5 + - - +
88f TYR* 2.8 68.8 + - + +
100f PHE 4.8 3.8 - - - +
101f GLY* 3.2 29.6 - - - +
102f GLY* 4.8 4.0 - - - -
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Residues in contact with ASP 85 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69f ALA* 4.5 2.7 - - - +
72f TYR* 3.2 41.2 - - + +
73f THR* 3.5 21.9 + - - +
76f ALA* 4.6 4.9 - - - +
78f ARG* 4.7 1.0 + - - -
81f VAL* 4.4 3.8 - - + -
82f THR* 2.5 42.4 + - - +
84f MET* 1.3 68.4 - - - +
86f VAL* 1.3 61.1 + - - +
88f TYR* 3.8 17.5 - - - -
89f ALA* 2.9 27.9 + - - +
80h TYR* 6.0 0.2 - - - +
81h ASN* 5.2 5.4 - - - +
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Residues in contact with VAL 86 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84e PHE* 6.1 1.3 - - + -
88e ALA* 4.0 18.4 - - + +
91e ALA* 4.4 17.0 - - + -
92e LEU* 3.7 35.7 - - + +
65f VAL* 5.4 3.0 - - + +
69f ALA* 4.8 8.7 - - + -
81f VAL* 4.1 13.2 - - + -
82f THR 3.3 15.3 - - - +
83f ALA* 3.2 8.7 + - - +
85f ASP* 1.3 76.9 - - - +
87f VAL* 1.3 63.2 + - - +
89f ALA* 3.3 6.8 + - - +
90f LEU* 3.0 38.4 + - + +
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Residues in contact with VAL 87 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91e ALA* 5.5 6.3 - - + -
83f ALA* 3.0 16.2 + - + +
84f MET* 3.0 9.4 + - - +
86f VAL* 1.3 77.8 - - + +
88f TYR* 1.3 62.9 + - + +
90f LEU* 3.1 14.3 + - + +
91f LYS* 2.9 29.8 + - + +
96f THR* 5.8 2.1 - - + -
97f LEU* 4.3 23.4 + - + +
98f TYR 6.1 0.2 - - - +
100f PHE* 4.6 17.3 - - + +
101f GLY 4.6 9.9 - - - +
102f GLY* 3.7 28.9 - - - +
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Residues in contact with TYR 88 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72f TYR* 3.5 19.0 + + + +
84f MET* 2.8 66.5 + - + +
85f ASP* 3.8 15.9 - - - -
87f VAL* 1.3 83.5 - - + +
89f ALA* 1.3 58.3 + - - +
91f LYS* 3.2 13.4 + - - +
92f ARG* 2.9 26.3 + - - +
102f GLY 5.1 10.1 - - - -
80h TYR* 3.5 77.4 + + + +
81h ASN* 6.0 0.2 - - - -
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Residues in contact with ALA 89 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65f VAL* 4.4 15.0 - - + +
68f ASP* 4.5 7.4 - - + -
69f ALA* 4.3 19.5 - - + +
72f TYR* 3.3 15.0 - - + -
85f ASP 2.9 17.9 + - - +
86f VAL* 3.7 5.6 - - - +
88f TYR* 1.3 73.0 - - - +
90f LEU* 1.3 62.5 + - - +
92f ARG* 3.1 9.1 + - - +
93f GLN* 3.0 30.0 + - - +
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Residues in contact with LEU 90 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91e ALA* 5.3 2.7 - - + +
92e LEU* 6.0 1.1 - - + -
95e ALA* 4.2 27.1 - - + -
61f PHE* 5.5 5.4 - - + -
65f VAL* 4.5 27.8 - - + -
86f VAL* 3.0 31.9 + - + +
87f VAL* 3.1 13.4 + - + +
89f ALA* 1.3 77.4 - - - +
91f LYS* 1.3 55.6 + - - +
93f GLN* 3.3 3.8 + - + -
94f GLY 3.1 4.0 + - - -
95f ARG* 2.6 63.1 + - + +
96f THR* 5.1 1.1 - - - -
97f LEU* 4.2 20.4 - - + +
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Residues in contact with LYS 91 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65d ASP* 4.1 15.4 + - - -
68d GLU* 4.0 20.9 + - - +
87f VAL* 2.9 16.0 + - + +
88f TYR* 3.2 14.6 + - - +
90f LEU* 1.3 76.1 - - - +
92f ARG* 1.3 58.4 + - - +
94f GLY* 2.8 18.9 + - - -
95f ARG 4.6 0.2 - - - -
96f THR* 3.9 35.3 + - + +
102f GLY 5.1 9.2 - - - -
76h ARG* 4.9 12.3 - - - +
80h TYR* 3.5 26.5 - - + +
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Residues in contact with ARG 92 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68f ASP* 3.8 20.2 + - - -
72f TYR* 4.2 8.7 - - + +
88f TYR 2.9 13.1 + - - +
89f ALA* 3.1 13.2 + - - +
91f LYS* 1.3 78.9 - - - +
93f GLN* 1.3 85.1 + - - +
94f GLY 3.5 0.5 + - - -
73h GLU* 4.2 23.3 - - - +
97h LEU* 2.5 36.3 + - + -
98h LEU* 3.4 30.8 + - + +
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Residues in contact with GLN 93 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64f ASN* 5.5 15.8 - - + +
65f VAL* 5.5 13.7 - - + -
68f ASP* 4.8 6.0 + - + +
89f ALA 3.0 16.0 + - - +
90f LEU* 3.3 3.5 + - + +
92f ARG* 1.3 108.7 - - - +
94f GLY* 1.3 63.4 + - - +
95f ARG* 3.3 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