Contacts of the helix formed by residues 85 - 101 (chain C) in PDB entry 3FB7
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 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ALA 3.4 22.4 + - - +
51C GLU* 2.8 19.1 + - - +
54C ALA* 3.3 33.9 - - + -
84C VAL* 1.3 82.3 - - - +
86C LEU* 1.3 60.3 + - - +
87C TRP* 3.6 3.6 + - - +
88C GLY* 2.8 22.7 + - - -
89C ARG* 3.2 24.1 + - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 1.3 72.0 - - - +
87C TRP* 1.3 91.2 + - + +
88C GLY 3.1 1.1 - - - -
89C ARG* 3.0 12.9 + - + +
90C CYS* 3.0 31.7 + - - -
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 6.3 1.3 - - - -
50C ALA* 4.1 17.5 - - + +
85C THR* 3.6 2.6 + - - +
86C LEU* 1.3 92.0 - - + +
88C GLY* 1.3 58.3 + - - +
90C CYS* 2.8 26.5 + - + +
91C VAL* 2.7 38.6 + - + +
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA* 5.3 2.5 - - - +
50C ALA* 3.7 13.8 - - - +
51C GLU* 3.5 14.1 - - - -
68C TRP* 4.6 2.8 - - - -
83C PRO* 3.6 11.5 - - - +
85C THR* 2.8 20.9 + - - -
87C TRP* 1.3 77.5 - - - +
89C ARG* 1.3 56.7 + - - +
91C VAL* 3.4 6.0 + - - +
92C ALA* 2.9 25.5 + - - +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 5.6 4.2 - - - -
83C PRO* 3.6 31.5 + - + -
84C VAL* 3.8 24.0 + - - +
85C THR 3.2 14.3 + - - +
86C LEU* 3.0 15.1 + - + +
88C GLY* 1.3 75.2 - - - +
90C CYS* 1.3 59.2 + - - +
92C ALA* 3.0 9.3 - - + +
93C VAL* 2.8 35.5 + - + +
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Residues in contact with CYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LEU* 3.0 33.5 + - - -
87C TRP* 2.8 37.5 + - + +
89C ARG* 1.3 73.1 - - - +
91C VAL* 1.3 67.6 + - + +
92C ALA 2.9 1.1 - - - -
93C VAL* 2.9 19.4 + - - +
94C VAL* 2.9 19.2 + - + +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY* 3.7 25.8 - - - +
46C LEU* 3.9 38.1 - - + +
47C ALA* 4.1 10.5 - - + +
50C ALA* 4.5 4.5 - - + -
68C TRP* 4.8 1.8 - - + -
87C TRP* 2.7 23.5 + - + +
88C GLY* 3.5 8.7 - - - +
90C CYS* 1.3 72.2 - - + +
92C ALA* 1.3 53.1 + - - +
94C VAL* 3.3 9.9 + - + +
95C VAL* 2.7 48.6 + - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TRP* 3.9 20.6 - - + -
72C THR* 4.6 0.2 - - - +
83C PRO* 4.0 15.0 - - + -
88C GLY 2.9 15.3 + - - +
89C ARG* 3.0 17.3 - - + +
91C VAL* 1.3 76.6 - - - +
93C VAL* 1.3 57.4 + - - +
95C VAL* 3.0 5.1 + - - +
96C MET* 2.9 49.1 + - + +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ARG* 2.8 25.8 + - + +
90C CYS* 2.9 9.1 + - - +
92C ALA* 1.3 72.2 - - - +
94C VAL* 1.3 64.3 + - + +
96C MET* 3.2 20.5 + - + +
97C VAL* 3.0 43.0 + - + +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 5.2 4.9 - - + -
90C CYS* 2.9 19.2 + - + +
91C VAL* 3.5 13.0 - - + +
93C VAL* 1.3 77.5 - - + +
95C VAL* 1.3 60.3 + - + +
97C VAL* 3.9 3.5 - - - +
98C ALA* 2.9 39.5 + - + +
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 4.0 21.0 - - + +
40C LEU* 5.1 2.2 - - + -
43C GLY* 4.2 15.0 - - - -
68C TRP* 4.6 7.0 - - + -
69C SER* 4.0 31.9 - - - +
72C THR* 4.4 13.0 - - + -
73C ALA* 4.5 7.0 - - + +
91C VAL* 2.7 37.8 + - + +
92C ALA* 3.0 8.7 + - - +
94C VAL* 1.3 78.0 - - + +
96C MET* 1.3 53.0 + - - +
98C ALA 3.8 0.2 - - - -
99C GLY* 2.8 32.1 + - - -
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Residues in contact with MET 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C THR* 3.6 28.7 - - + +
73C ALA* 5.2 0.4 - - - +
92C ALA* 2.9 47.5 + - + +
93C VAL* 3.2 22.6 + - + +
95C VAL* 1.3 76.6 - - - +
97C VAL* 1.3 57.0 + - + +
100C ILE* 2.6 51.5 + - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C VAL* 3.0 30.9 + - + +
94C VAL* 3.9 3.6 - - - +
96C MET* 1.3 73.9 - - + +
98C ALA* 1.3 59.4 + - + +
99C GLY 2.8 8.7 + - - -
100C ILE* 4.3 1.3 - - - +
101C THR* 2.6 39.5 + - - +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 4.5 8.2 - - + +
39C VAL* 4.1 26.2 - - + +
94C VAL* 2.9 24.2 + - + +
95C VAL 3.8 0.2 - - - -
97C VAL* 1.3 79.3 - - + +
99C GLY* 1.3 51.1 + - - +
101C THR* 4.5 4.3 - - - -
102C SER* 2.7 32.9 + - - -
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.2 7.8 - - - +
39C VAL* 5.1 3.4 - - - -
73C ALA* 4.1 18.8 - - - +
95C VAL 2.8 22.8 + - - -
97C VAL 2.8 1.8 - - - -
98C ALA* 1.3 79.5 - - - +
100C ILE* 1.3 57.4 + - - -
101C THR 3.2 0.9 - - - -
102C SER* 3.6 4.5 - - - -
103C PHE* 2.9 28.1 + - - +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ALA 4.0 7.4 - - - +
75C THR* 3.7 31.6 - - + -
96C MET* 2.6 35.9 + - + +
97C VAL* 4.3 1.6 - - - +
99C GLY* 1.3 69.4 - - - +
101C THR* 1.3 68.9 + - - +
103C PHE* 3.2 16.3 + - - +
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 6.2 2.5 - - + -
97C VAL* 2.6 29.7 + - - +
98C ALA* 4.5 4.3 - - - -
100C ILE* 1.3 77.7 - - - +
102C SER* 1.3 57.5 + - - +
103C PHE 2.7 15.0 + - - -
104C GLY* 2.9 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