Contacts of the helix formed by residues 71 - 84 (chain F) in PDB entry 2FRV
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 VAL 71 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F CYS* 3.3 24.5 - - + +
69F THR 3.2 8.2 + - - +
70F TYR* 1.3 72.4 - - + +
72F HIS* 1.3 61.8 + - + +
74F LEU* 3.4 5.0 - - - +
75F ALA* 3.1 21.3 + - - +
100F MET* 3.6 34.8 - - + -
103F GLN* 4.1 7.4 - - + -
459F VAL* 3.9 3.2 - - + +
461F ALA* 3.9 7.2 - - + -
462F PRO* 3.8 23.8 - - + -
466F LEU* 3.6 13.6 - - + +
537F FCO 3.6 24.5 - - - +
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Residues in contact with HIS 72 (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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61F THR* 3.3 31.8 + - - +
62F GLN* 3.8 6.3 - - + -
64F ALA* 4.1 10.5 - - + +
65F CYS* 4.6 5.4 - - + -
68F CYS* 4.1 11.6 + - - -
70F TYR 3.2 1.0 - - - +
71F VAL* 1.3 81.9 - - + +
73F ALA* 1.3 66.2 + - - +
74F LEU 3.2 0.4 - - - -
76F SER* 3.2 21.3 + - - -
466F LEU* 3.7 23.7 - - + +
468F HIS* 2.9 33.5 + - + -
482F LEU* 3.9 9.6 - - + +
484F VAL* 4.0 15.9 - - + -
533F CYS* 3.5 23.1 - - + -
537F FCO 3.6 6.1 - - - -
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Residues in contact with ALA 73 (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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58F GLN* 3.9 29.6 - - - +
62F GLN* 3.7 32.3 - - - +
70F TYR* 2.8 17.6 + - + +
72F HIS* 1.3 80.8 - - - +
74F LEU* 1.3 54.8 + - - +
76F SER* 3.5 1.9 - - - -
77F VAL* 2.9 34.5 + - - +
220F THR* 4.6 1.6 - - - +
223F THR* 4.2 7.9 - - - +
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Residues in contact with LEU 74 (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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70F TYR* 3.1 38.6 + - + +
71F VAL* 3.4 9.2 - - - +
73F ALA* 1.3 74.0 - - - +
75F ALA* 1.3 60.9 + - - +
77F VAL* 3.4 6.6 + - + +
78F ARG* 2.8 80.2 + - + +
96F ARG* 4.1 23.6 - - + +
100F MET* 3.6 30.5 - - + -
223F THR* 5.4 0.9 - - + -
285F GLU* 4.4 1.6 - - - +
459F VAL* 3.8 7.4 - - + -
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Residues in contact with ALA 75 (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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71F VAL 3.1 12.2 + - - +
72F HIS 3.6 0.2 + - - -
73F ALA 3.5 0.2 - - - -
74F LEU* 1.3 77.9 - - - +
76F SER* 1.3 56.3 + - - +
78F ARG* 3.4 2.6 + - - -
79F ALA* 3.0 29.5 + - - +
457F GLY* 3.6 13.5 - - - +
459F VAL* 3.5 22.4 - - + +
466F LEU* 4.1 8.5 - - + -
468F HIS* 3.5 33.2 - - + +
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Residues in contact with SER 76 (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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57F ALA* 4.3 1.9 + - - -
58F GLN* 3.8 16.2 - - - -
61F THR* 3.0 18.2 + - - +
72F HIS 3.2 14.5 + - - -
73F ALA 3.5 3.8 - - - -
74F LEU 3.1 0.6 - - - -
75F ALA* 1.3 72.7 - - - +
77F VAL* 1.3 60.3 + - - +
78F ARG 3.1 1.3 - - - -
79F ALA* 3.2 2.3 + - - +
80F VAL* 3.0 35.3 + - - +
468F HIS* 2.8 20.2 + - - -
480F PHE* 3.1 21.3 - - - -
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Residues in contact with VAL 77 (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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58F GLN* 3.5 42.6 - - + +
73F ALA 2.9 14.7 + - - +
74F LEU* 3.5 16.4 - - + +
76F SER* 1.3 74.6 - - - +
78F ARG* 1.3 60.3 + - - +
80F VAL* 3.9 0.6 - - - +
81F ASP* 2.9 36.2 + - - +
96F ARG* 3.5 30.3 - - - +
223F THR* 4.2 6.7 - - - +
224F VAL* 3.8 23.8 - - - +
225F VAL* 4.0 10.8 - - + +
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Residues in contact with ARG 78 (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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74F LEU* 2.8 53.3 + - + +
75F ALA 3.8 4.5 - - - +
76F SER 3.1 0.2 - - - -
77F VAL* 1.3 78.6 - - - +
79F ALA* 1.3 56.3 + - - +
81F ASP* 3.9 6.2 - - - +
82F ASN* 3.2 27.5 + - - +
96F ARG* 4.1 12.9 + - - +
97F ASN* 4.2 7.7 + - - -
285F GLU* 3.0 30.7 + - - -
287F PRO* 3.6 18.2 - - - +
290F GLU* 3.7 20.7 + - - +
296F ARG* 3.6 15.4 - - - +
456F VAL 4.0 1.2 - - - +
457F GLY* 3.8 10.8 - - - -
458F PHE 3.0 28.9 + - - +
459F VAL* 3.6 12.7 - - - +
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Residues in contact with ALA 79 (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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75F ALA 3.0 16.6 + - - +
76F SER* 3.2 5.4 + - - +
78F ARG* 1.3 77.5 - - - +
80F VAL* 1.3 59.3 + - + +
83F CYS* 3.1 26.5 + - - +
455F GLY* 3.7 3.3 - - - -
456F VAL* 3.7 6.3 - - - -
457F GLY 3.6 9.0 - - - +
468F HIS* 3.3 33.7 - - + +
470F ILE* 3.5 17.0 - - + +
480F PHE* 5.0 1.6 - - + -
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Residues in contact with VAL 80 (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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54F PRO* 3.9 34.5 - - + +
55F ARG 5.2 0.2 - - - +
57F ALA* 5.1 1.1 - - + -
76F SER 3.0 19.1 + - - +
77F VAL 4.3 0.2 - - - +
79F ALA* 1.3 75.8 - - - +
81F ASP* 1.3 65.0 + - - +
83F CYS* 3.4 10.1 + - - +
84F VAL* 3.1 28.5 + - + +
225F VAL* 3.8 30.7 - - + -
447F TRP* 5.3 1.3 - - + -
449F TYR* 4.8 11.0 - - + -
470F ILE* 4.2 18.8 - - + -
480F PHE* 4.7 8.7 - - + -
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Residues in contact with ASP 81 (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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77F VAL 2.9 24.7 + - - +
78F ARG* 3.9 6.2 - - - +
80F VAL* 1.3 77.6 - - - +
82F ASN* 1.3 61.3 + - - +
84F VAL* 3.2 0.9 + - - +
85F GLY 3.0 18.7 + - - -
86F VAL* 3.2 29.1 + - + +
88F ILE* 3.3 18.0 - - + +
96F ARG* 2.8 29.6 + - - -
224F VAL 4.0 0.3 - - - +
225F VAL* 3.1 11.6 - - - -
226F GLY 2.9 27.4 + - - -
290F GLU* 5.3 0.9 - - - +
291F TYR* 3.7 4.7 - - + -
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Residues in contact with ASN 82 (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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78F ARG 3.2 18.7 + - - +
79F ALA 3.8 4.5 - - - +
81F ASP* 1.3 77.1 - - - +
83F CYS* 1.3 62.1 + - - +
84F VAL 3.3 1.0 + - - -
85F GLY* 3.6 9.0 + - - -
290F GLU 5.6 0.5 - - - +
291F TYR* 3.4 34.9 + - + -
337F TYR* 4.7 1.0 + - - -
454F GLN 4.4 2.5 + - - +
455F GLY* 3.3 9.7 - - - -
456F VAL* 3.0 39.9 + - - +
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Residues in contact with CYS 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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79F ALA 3.1 8.5 + - - +
80F VAL* 3.4 12.7 + - - -
81F ASP 3.3 0.8 - - - -
82F ASN* 1.3 80.2 - - - +
84F VAL* 1.3 60.5 + - - +
85F GLY 3.6 0.4 - - - -
449F TYR* 5.7 0.4 - - - -
450F PRO* 3.4 3.6 - - - +
453F SER* 2.6 44.8 + - - +
454F GLN 3.2 34.3 - - - +
455F GLY* 3.3 5.8 - - - +
470F ILE* 4.0 15.9 - - + -
472F GLN* 3.7 20.2 - - - -
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Residues in contact with VAL 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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80F VAL* 3.1 16.8 + - + +
81F ASP 3.6 7.9 - - - +
82F ASN 3.2 0.6 - - - -
83F CYS* 1.3 76.6 - - - +
85F GLY* 1.3 57.6 + - - +
86F VAL* 3.4 21.9 + - + +
225F VAL* 4.8 0.7 - - + -
447F TRP* 3.6 47.4 - - + +
448F GLN 3.7 18.6 + - - +
449F TYR* 3.9 11.9 - - + -
450F PRO* 3.8 20.2 - - + +
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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