Contacts of the helix formed by residues 71 - 84 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J CYS* 3.3 24.2 - - + +
69J THR 3.2 8.2 + - - +
70J TYR* 1.3 72.0 - - + +
72J HIS* 1.3 60.4 + - + +
74J LEU* 3.4 5.3 - - - +
75J ALA* 3.1 21.1 + - - +
100J MET* 3.6 34.3 - - + -
103J GLN* 4.1 6.5 - - + -
459J VAL* 3.9 3.2 - - + +
461J ALA* 3.9 7.4 - - + -
462J PRO* 3.8 23.8 - - + -
466J LEU* 3.6 14.9 - - + +
537J FCO 3.6 24.2 - - - +
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Residues in contact with HIS 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J THR* 3.3 30.4 + - - +
62J GLN* 3.8 6.1 - - + -
64J ALA* 4.1 11.3 - - + +
65J CYS* 4.6 5.2 - - + -
68J CYS* 4.1 12.1 + - - -
70J TYR 3.2 1.2 - - - +
71J VAL* 1.3 82.6 - - + +
73J ALA* 1.3 66.2 - - - +
74J LEU 3.2 0.2 - - - -
76J SER* 3.2 20.3 + - - -
466J LEU* 3.7 23.3 - - + +
468J HIS* 2.9 34.0 + - + -
482J LEU* 3.9 9.6 - - + +
484J VAL* 4.0 15.9 - - + -
533J CYS* 3.5 22.8 - - + -
537J FCO 3.6 6.4 - - - -
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Residues in contact with ALA 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 3.9 29.6 - - - +
62J GLN* 3.7 32.1 - - - +
70J TYR* 2.8 18.4 + - + +
72J HIS* 1.3 78.7 - - - +
74J LEU* 1.3 55.3 + - - +
76J SER* 3.2 2.6 + - - -
77J VAL* 2.9 33.3 + - - +
220J THR* 4.6 1.8 - - - +
223J THR* 4.2 7.6 - - - +
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Residues in contact with LEU 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J TYR* 3.1 40.2 + - + +
71J VAL 3.4 9.4 - - - +
73J ALA* 1.3 74.0 - - - +
75J ALA* 1.3 60.0 + - - +
77J VAL* 3.4 7.3 + - + +
78J ARG* 2.8 79.3 + - + +
96J ARG* 4.1 22.7 - - + +
100J MET* 3.6 30.1 - - + -
223J THR* 5.4 0.7 - - + -
285J GLU* 4.4 1.6 - - - +
459J VAL* 3.8 8.3 - - + -
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Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL 3.1 11.2 + - - +
73J ALA 3.5 0.2 - - - -
74J LEU* 1.3 78.2 - - - +
76J SER* 1.3 56.3 + - - +
78J ARG* 4.4 2.9 - - - -
79J ALA* 3.0 29.8 + - - +
457J GLY* 3.6 12.9 - - - +
459J VAL* 3.5 22.6 - - + +
466J LEU* 4.1 9.2 - - + -
468J HIS* 3.5 33.7 - - + +
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Residues in contact with SER 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J ALA* 4.3 1.3 + - - -
58J GLN* 3.8 17.0 - - - -
61J THR* 3.0 18.6 + - - +
72J HIS 3.2 15.6 + - - -
73J ALA 3.5 3.1 - - - -
74J LEU 3.1 0.6 - - - -
75J ALA* 1.3 72.8 - - - +
77J VAL* 1.3 60.3 + - - +
78J ARG 3.1 1.1 - - - -
79J ALA* 3.2 2.4 + - - +
80J VAL* 3.0 35.7 + - - +
468J HIS* 2.8 20.5 + - - -
480J PHE* 3.1 20.9 - - - -
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Residues in contact with VAL 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 3.5 42.6 - - + +
73J ALA 2.9 15.8 + - - +
74J LEU* 3.5 16.4 - - + +
76J SER* 1.3 73.6 - - - +
78J ARG* 1.3 58.8 + - - +
80J VAL* 4.3 0.6 - - - +
81J ASP* 2.9 37.2 + - - +
96J ARG* 3.5 29.6 - - - +
223J THR* 4.2 6.7 - - - +
224J VAL* 3.8 23.1 - - - +
225J VAL* 4.0 10.8 - - + +
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Residues in contact with ARG 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J LEU* 2.8 54.4 + - + +
75J ALA 3.8 4.0 - - - +
77J VAL* 1.3 77.4 - - - +
79J ALA* 1.3 57.3 + - - +
81J ASP* 3.9 6.2 - - - +
82J ASN* 3.2 27.7 + - - +
96J ARG* 4.1 13.1 + - - +
97J ASN* 4.2 7.7 + - - -
285J GLU* 3.0 29.7 + - - -
287J PRO* 3.6 19.0 - - - +
290J GLU* 3.7 19.9 + - - +
296J ARG* 3.6 14.9 - - - +
456J VAL 4.0 1.6 - - - +
457J GLY* 3.8 10.5 - - - -
458J PHE 3.0 30.0 + - - +
459J VAL* 3.6 12.5 - - - +
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Residues in contact with ALA 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ALA 3.0 16.4 + - - +
76J SER* 3.2 5.1 + - - +
78J ARG* 1.3 76.8 - - - +
80J VAL* 1.3 59.2 + - + +
82J ASN* 3.8 0.6 - - - +
83J CYS* 3.1 26.5 + - - +
455J GLY* 3.7 3.5 - - - -
456J VAL* 3.7 5.6 - - - -
457J GLY* 3.6 9.2 - - - +
468J HIS* 3.3 33.2 - - + +
470J ILE* 3.5 16.7 - - + +
480J PHE* 5.0 1.8 - - + -
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Residues in contact with VAL 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J PRO* 3.9 35.9 - - + +
55J ARG 5.2 0.2 - - - +
57J ALA* 5.1 1.1 - - + -
76J SER 3.0 19.8 + - - +
79J ALA* 1.3 76.2 - - - +
81J ASP* 1.3 65.6 + - - +
83J CYS* 3.4 10.3 + - - +
84J VAL* 3.1 29.0 + - + +
225J VAL* 3.8 31.2 - - + -
447J TRP* 5.3 1.6 - - + -
449J TYR* 4.8 10.1 - - + -
470J ILE* 4.2 18.8 - - + -
480J PHE* 4.7 8.5 - - + -
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Residues in contact with ASP 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J VAL 2.9 25.3 + - - +
78J ARG* 3.9 5.0 - - - +
79J ALA 3.4 0.2 - - - -
80J VAL* 1.3 75.7 - - - +
82J ASN* 1.3 62.3 + - - +
84J VAL* 3.2 0.9 + - - +
85J GLY 3.0 18.7 + - - -
86J VAL* 3.2 28.7 + - + +
88J ILE* 3.3 17.2 - - + +
96J ARG* 2.8 30.7 + - - -
224J VAL 4.0 0.5 - - - +
225J VAL* 3.1 12.1 - - - -
226J GLY 2.9 27.7 + - - -
290J GLU* 5.3 0.9 - - - +
291J TYR* 3.7 5.2 - - + +
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Residues in contact with ASN 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ARG 3.2 18.9 + - - +
79J ALA 3.8 4.0 - - - +
81J ASP* 1.3 77.5 - - - +
83J CYS* 1.3 62.0 + - - +
84J VAL 3.3 0.7 + - - -
85J GLY* 3.6 8.8 + - - -
290J GLU 5.6 0.7 - - - +
291J TYR* 3.4 34.4 + - + -
337J TYR* 4.7 1.4 + - - -
454J GLN 4.4 2.3 + - - +
455J GLY* 3.3 9.5 - - - -
456J VAL* 3.0 40.4 + - - +
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Residues in contact with CYS 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J ALA 3.1 9.4 + - - +
80J VAL* 3.4 13.2 + - - -
81J ASP 3.3 0.8 - - - -
82J ASN* 1.3 79.5 - - - +
84J VAL* 1.3 60.3 + - - +
85J GLY 3.6 0.4 - - - -
449J TYR* 5.7 0.4 - - - -
450J PRO* 3.4 3.3 - - - +
453J SER* 2.6 46.1 + - - +
454J GLN 3.2 33.4 - - - +
455J GLY* 3.3 6.7 - - - +
470J ILE* 4.0 15.0 - - + -
472J GLN* 3.7 19.3 - - - -
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Residues in contact with VAL 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J VAL* 3.1 15.7 - - + +
81J ASP 3.6 8.5 - - - +
82J ASN 3.2 0.2 - - - -
83J CYS* 1.3 77.6 - - - +
85J GLY* 1.3 57.9 + - - +
86J VAL* 3.4 22.2 + - + +
225J VAL* 4.8 0.9 - - + -
447J TRP* 3.6 46.9 - - + +
448J GLN 3.7 18.0 + - - +
449J TYR* 3.9 12.1 - - + -
450J PRO* 3.8 19.5 - - + +
128L ASN* 5.5 3.1 - - - +
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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