Contacts of the helix formed by residues 54 - 64 (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 PRO 54 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52L ARG 3.5 5.3 - - - +
53L ASP* 1.3 88.1 - - - +
55L ARG* 1.3 58.5 + - - +
56L ASP 3.4 0.7 + - - -
57L ALA* 3.4 17.4 + - + +
58L GLN 4.6 1.0 + - - -
80L VAL* 3.9 25.6 - - + +
225L VAL* 4.9 1.6 - - - +
449L TYR* 3.5 20.2 - - + +
470L ILE* 3.7 23.1 - - + -
472L GLN* 4.3 8.5 - - + -
475L GLY 3.1 27.6 - - - +
476L LYS 4.2 1.3 - - - +
477L ILE* 3.8 22.7 - - + -
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Residues in contact with ARG 55 (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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53L ASP* 2.8 18.4 + - - +
54L PRO* 1.3 75.4 - - - +
56L ASP* 1.3 61.8 + - - +
58L GLN* 4.3 8.9 + - - +
59L HIS* 3.9 6.1 + - - -
224L VAL* 5.4 3.0 - - - +
225L VAL* 4.7 15.6 - - + +
444L TYR* 4.7 8.0 + - - -
447L TRP* 3.8 32.5 - - + +
449L TYR* 3.7 13.2 - - - +
203S PHE* 3.9 18.2 - - - -
217S LEU* 5.4 3.6 - - - +
262S TYR* 3.4 71.9 + - + +
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Residues in contact with ASP 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L ARG* 5.2 7.4 - - + +
53L ASP* 2.8 25.9 + - + +
55L ARG* 1.3 78.9 - - - +
57L ALA* 1.3 67.1 + - - +
58L GLN 3.2 2.0 - - - -
59L HIS* 2.8 23.4 + - - +
60L PHE* 3.5 22.6 + - + -
259S SER* 3.7 7.4 - - - -
260S PRO* 3.2 24.9 - - - +
261S PHE* 3.0 38.6 + - + +
262S TYR* 4.6 1.9 + - - -
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Residues in contact with ALA 57 (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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49L LEU* 4.4 13.9 - - + -
52L ARG* 6.0 0.6 - - - +
53L ASP 3.5 3.6 + - - -
54L PRO* 3.4 16.8 + - + +
56L ASP* 1.3 76.7 - - - +
58L GLN* 1.3 63.8 + - - +
60L PHE* 3.1 2.9 + - - +
61L THR* 2.8 29.5 + - + +
76L SER* 4.3 3.1 - - - +
80L VAL* 5.1 2.5 - - + -
477L ILE* 4.4 8.5 - - + +
480L PHE* 3.6 35.9 - - + -
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Residues in contact with GLN 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L PRO 4.6 1.4 + - - -
55L ARG 4.3 7.3 + - - +
56L ASP 3.0 1.4 + - - -
57L ALA* 1.3 79.7 - - - +
59L HIS* 1.3 77.7 + - + +
61L THR* 3.2 7.5 + - - -
62L GLN* 3.1 30.9 + - - +
73L ALA* 3.9 27.5 - - - +
76L SER* 3.8 8.9 - - - -
77L VAL* 3.5 15.0 - - + +
223L THR* 2.7 51.9 + - - +
224L VAL* 3.5 9.5 - - - +
225L VAL* 4.5 2.6 - - + +
262S TYR* 3.3 15.6 + - - -
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Residues in contact with HIS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ARG 3.9 11.0 - - - -
56L ASP 2.8 15.3 + - - +
58L GLN* 1.3 85.3 - - + +
60L PHE* 1.3 64.2 + - - +
62L GLN* 3.9 4.7 + - - +
63L ARG* 3.3 36.8 + - - +
220L THR 5.8 0.6 + - - -
221L GLN* 4.7 9.3 - - + +
244S HIS* 3.5 22.6 - + - -
247S ILE* 4.3 22.7 - - + +
255S TRP* 3.4 5.9 - - + -
261S PHE* 3.7 39.3 - + + +
262S TYR* 2.8 33.2 + + - -
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Residues in contact with PHE 60 (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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45L LEU* 3.8 13.9 - - + +
48L ILE* 3.7 32.5 - - + -
49L LEU* 3.5 25.8 - - + -
52L ARG* 3.6 24.7 - - - -
56L ASP* 3.6 22.2 - - + -
57L ALA 3.1 2.6 + - - +
59L HIS* 1.3 78.3 - - - +
61L THR* 1.3 64.0 + - - +
63L ARG* 3.2 19.4 + - - +
118S VAL* 4.0 12.3 - - + +
121S ALA* 3.8 13.0 - - + -
255S TRP* 3.5 52.0 - + - -
259S SER* 4.8 1.6 - - - -
261S PHE* 4.1 15.0 - + - -
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Residues in contact with THR 61 (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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45L LEU* 4.5 9.0 - - + -
49L LEU* 3.8 26.2 - - + -
57L ALA 2.8 21.9 + - - +
58L GLN* 3.2 7.4 + - - -
60L PHE* 1.3 67.1 - - - +
62L GLN* 1.3 69.5 + - - +
63L ARG 3.0 1.8 - - - -
64L ALA* 2.9 22.4 + - - +
72L HIS* 3.3 14.2 + - - +
76L SER* 3.0 25.2 + - - +
468L HIS* 3.8 11.9 - - + -
480L PHE* 4.0 11.2 - - + -
482L LEU* 4.0 11.9 - - + -
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Residues in contact with GLN 62 (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* 3.1 15.9 + - - +
59L HIS* 4.0 10.0 + - - +
60L PHE 3.2 0.2 - - - -
61L THR* 1.3 85.0 + - - +
63L ARG* 1.3 72.4 + - - +
64L ALA 3.1 2.3 + - - -
65L CYS 3.1 23.2 + - - +
69L THR* 5.1 0.2 - - - -
70L TYR* 2.9 30.6 + - - +
72L HIS* 3.8 12.1 - - + -
73L ALA* 3.7 22.4 - - + +
219L HIS* 3.4 13.9 - - - +
220L THR* 3.0 44.3 + - - +
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Residues in contact with ARG 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ARG* 2.8 21.7 + - - -
45L LEU* 4.3 2.1 - - - +
59L HIS* 3.3 28.6 + - - +
60L PHE 3.2 11.6 + - - +
61L THR 3.0 1.0 - - - -
62L GLN* 1.3 94.2 - - - +
64L ALA* 1.3 61.8 + - - +
65L CYS 3.0 2.5 - - - +
216L LYS* 4.3 6.9 - - - +
219L HIS* 3.5 28.8 + - - +
220L THR 5.0 1.6 + - - -
221L GLN* 4.6 5.3 + - - -
17S CYS* 3.2 7.2 - - - +
118S VAL* 4.0 11.6 - - + +
148S CYS* 3.0 39.1 + - - +
247S ILE* 4.3 18.3 - - - +
249S CYS* 4.8 3.6 - - - +
255S TRP* 3.7 18.9 - - + -
267S SF4 3.6 26.2 - - - -
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Residues in contact with ALA 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ARG* 2.7 27.1 + - - +
45L LEU* 3.6 18.3 - - + +
61L THR 2.9 17.9 + - - +
63L ARG* 1.3 80.4 - - - +
65L CYS* 1.3 59.3 + - - +
72L HIS* 4.1 20.9 - - + +
482L LEU* 4.4 3.8 - - + -
532L ALA* 3.1 19.7 - - - +
533L CYS* 5.0 1.3 - - - -
536L HIS* 4.3 13.5 - - + -
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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