Contacts of the helix formed by residues 71 - 84 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68L CYS* 3.3 24.7 - - + +
69L THR 3.2 8.5 + - - +
70L TYR* 1.3 73.1 - - + +
72L HIS* 1.3 61.9 + - + +
74L LEU* 3.4 4.6 - - - +
75L ALA* 3.1 21.0 + - - +
100L MET* 3.6 34.8 - - + -
103L GLN* 4.1 7.2 - - + -
459L VAL* 3.9 3.0 - - + +
461L ALA* 3.9 7.4 - - + -
462L PRO* 3.8 23.3 - - + -
466L LEU* 3.6 13.9 - - + +
537L FCO 3.6 24.0 - - - +
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Residues in contact with HIS 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L THR* 3.3 29.8 + - - +
62L GLN* 3.8 6.1 - - + -
64L ALA* 4.1 10.9 - - + +
65L CYS* 4.6 5.2 - - + -
68L CYS* 4.1 11.4 + - - -
70L TYR 3.2 1.2 - - - +
71L VAL* 1.3 83.2 - - + +
73L ALA* 1.3 66.9 + - - +
74L LEU 3.2 0.2 - - - -
75L ALA 3.9 0.2 - - - -
76L SER* 3.2 21.3 + - - -
466L LEU* 3.7 23.5 - - + +
468L HIS* 2.9 34.5 + - + -
482L LEU* 3.9 9.2 - - + +
484L VAL* 4.0 15.9 - - + -
533L CYS* 3.5 22.5 - - + -
537L FCO 3.6 6.1 - - - -
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Residues in contact with ALA 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L GLN* 3.9 28.8 - - - +
62L GLN* 3.7 31.6 - - - +
70L TYR* 2.8 19.1 + - + +
72L HIS* 1.3 79.9 - - - +
74L LEU* 1.3 54.9 + - - +
76L SER* 3.5 1.9 - - - -
77L VAL* 2.9 34.8 + - - +
220L THR* 4.6 2.2 - - - +
223L THR* 4.2 8.5 - - - +
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L TYR* 3.1 40.0 + - + +
71L VAL* 3.4 9.9 - - - +
73L ALA* 1.3 72.8 - - - +
75L ALA* 1.3 59.7 + - - +
77L VAL* 3.4 7.8 + - + +
78L ARG* 2.8 80.2 + - + +
96L ARG* 4.1 23.3 - - + +
100L MET* 3.6 30.3 - - + -
223L THR* 5.4 0.9 - - + -
285L GLU* 4.4 1.6 - - - +
459L VAL* 3.8 7.2 - - + -
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Residues in contact with ALA 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L VAL 3.1 10.9 + - - +
72L HIS 3.6 0.2 + - - -
73L ALA 3.5 0.2 - - - -
74L LEU* 1.3 77.4 - - - +
76L SER* 1.3 56.1 + - - +
78L ARG* 3.4 3.3 + - - -
79L ALA* 3.0 28.9 + - - +
457L GLY* 3.6 13.7 - - - +
459L VAL* 3.5 22.8 - - + +
466L LEU* 4.1 8.7 - - + -
468L HIS* 3.5 34.5 - - + +
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Residues in contact with SER 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L ALA* 4.3 1.9 + - - -
58L GLN* 3.8 16.8 - - - -
61L THR* 3.0 18.9 + - - +
72L HIS 3.2 14.5 + - - -
73L ALA 3.5 3.8 - - - -
74L LEU 3.1 0.6 - - - -
75L ALA* 1.3 73.0 - - - +
77L VAL* 1.3 59.7 + - - +
78L ARG 3.1 1.1 - - - -
79L ALA* 3.2 2.1 + - - +
80L VAL* 3.0 35.7 + - - +
468L HIS* 2.8 20.2 + - - -
480L PHE* 3.1 20.0 - - - -
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Residues in contact with VAL 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L GLN* 3.5 42.4 - - + +
73L ALA 2.9 14.3 + - - +
74L LEU* 3.5 17.3 - - + +
76L SER* 1.3 74.2 - - - +
78L ARG* 1.3 59.4 + - - +
80L VAL* 3.9 0.7 - - - +
81L ASP* 2.9 36.9 + - - +
96L ARG* 3.5 30.1 - - - +
223L THR* 4.2 7.6 - - - +
224L VAL* 3.8 22.4 - - - +
225L VAL* 4.0 11.4 - - + +
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Residues in contact with ARG 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L LEU* 2.8 53.7 + - + +
75L ALA 3.8 4.3 - - - +
77L VAL* 1.3 78.3 - - - +
79L ALA* 1.3 55.5 + - - +
81L ASP* 3.9 6.8 - - - +
82L ASN* 3.2 27.7 + - - +
96L ARG* 4.1 12.9 + - - +
97L ASN* 4.2 7.7 + - - -
285L GLU* 3.0 30.7 + - - -
287L PRO* 3.6 18.6 - - - +
290L GLU* 3.7 19.5 + - - +
296L ARG* 3.6 14.7 - - - +
456L VAL 4.0 2.0 - - - +
457L GLY* 3.8 10.3 - - - -
458L PHE 3.0 29.3 + - - +
459L VAL* 3.6 12.7 - - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ALA 3.0 15.7 + - - +
76L SER* 3.2 5.3 + - - +
78L ARG* 1.3 76.2 - - - +
80L VAL* 1.3 60.1 + - + +
83L CYS* 3.1 26.3 + - - +
455L GLY* 3.7 3.5 - - - -
456L VAL* 3.7 7.2 - - - -
457L GLY* 3.6 9.8 - - - +
468L HIS* 3.3 33.0 - - + +
470L ILE* 3.5 16.8 - - + +
480L PHE* 5.0 1.8 - - + -
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Residues in contact with VAL 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PRO* 3.9 35.9 - - + +
55L ARG 5.2 0.2 - - - +
57L ALA* 5.1 1.1 - - + -
76L SER 3.0 19.3 + - - +
79L ALA* 1.3 76.0 - - - +
81L ASP* 1.3 66.4 + - - +
83L CYS* 3.4 10.1 + - - +
84L VAL* 3.1 28.6 + - + +
225L VAL* 3.8 31.0 - - + -
447L TRP* 5.3 1.6 - - + -
449L TYR* 4.8 10.1 - - + -
470L ILE* 4.2 18.6 - - + -
480L PHE* 4.7 7.9 - - + -
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Residues in contact with ASP 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L VAL 2.9 25.5 + - - +
78L ARG* 3.9 5.4 - - - +
80L VAL* 1.3 76.4 - - - +
82L ASN* 1.3 62.0 + - - +
84L VAL* 3.2 1.0 + - - +
85L GLY 3.0 19.1 + - - -
86L VAL* 3.2 27.9 + - + +
88L ILE* 3.3 17.6 - - + +
96L ARG* 2.8 30.3 + - - -
224L VAL 4.0 0.7 - - - +
225L VAL* 3.1 11.8 - - - -
226L GLY 2.9 28.0 + - - -
290L GLU* 5.3 0.9 - - - +
291L TYR* 3.7 5.2 - - + +
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Residues in contact with ASN 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L ARG 3.2 19.4 + - - +
79L ALA 3.8 4.0 - - - +
81L ASP* 1.3 76.8 - - - +
83L CYS* 1.3 61.5 + - - +
84L VAL 3.3 1.0 + - - -
85L GLY* 3.6 9.2 + - - -
290L GLU 5.6 0.5 - - - +
291L TYR* 3.4 34.4 + - + -
337L TYR* 4.7 1.0 + - - -
454L GLN 4.4 3.2 + - - +
455L GLY* 3.3 9.5 - - - -
456L VAL* 3.0 40.0 + - - +
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Residues in contact with CYS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L ALA 3.1 9.0 + - - +
80L VAL* 3.4 12.5 + - - -
81L ASP 3.3 0.6 - - - -
82L ASN* 1.3 80.0 - - - +
84L VAL* 1.3 61.4 + - - +
85L GLY 3.6 0.2 - - - -
449L TYR* 5.7 0.4 - - - -
450L PRO* 3.4 3.6 - - - +
453L SER* 2.6 45.1 + - - +
454L GLN 3.2 33.9 - - - +
455L GLY* 3.3 6.5 - - - +
470L ILE* 4.0 15.7 - - + -
472L GLN* 3.7 19.5 - - - -
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Residues in contact with VAL 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L VAL* 3.1 15.0 - - + +
81L ASP* 3.6 8.7 - - - +
82L ASN 3.2 0.4 - - - -
83L CYS* 1.3 77.3 - - - +
85L GLY* 1.3 57.5 + - - +
86L VAL* 3.6 21.7 - - + +
225L VAL* 4.8 0.9 - - + -
447L TRP* 3.6 48.9 - - + +
448L GLN 3.7 19.3 + - - +
449L TYR* 3.9 11.7 - - + -
450L PRO* 3.8 18.4 - - + +
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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