Contacts of the helix formed by residues 54 - 64 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ARG 3.5 4.9 - - - +
53B ASP* 1.3 87.1 - - - +
55B ARG* 1.3 58.0 + - - +
56B ASP 3.4 0.9 + - - -
57B ALA* 3.4 17.1 + - + +
58B GLN 4.6 1.0 + - - -
80B VAL* 3.9 26.3 - - + +
83B CYS* 6.2 0.2 - - - -
225B VAL* 4.9 1.4 - - - +
449B TYR* 3.5 20.6 - - + +
470B ILE* 3.7 22.9 - - + -
472B GLN* 4.3 9.0 - - + -
475B GLY 3.1 27.8 - - - +
476B LYS 4.2 1.8 - - - +
477B ILE* 3.8 22.7 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE* 3.9 18.0 - - - -
217A LEU* 5.4 3.4 - - - +
262A TYR* 3.4 72.8 + - + +
53B ASP* 2.8 19.3 + - - +
54B PRO* 1.3 76.4 - - - +
56B ASP* 1.3 60.8 + - - +
58B GLN* 4.3 9.3 + - - +
59B HIS* 3.9 5.9 + - - -
80B VAL* 5.9 0.2 - - + -
224B VAL* 5.4 3.2 - - - +
225B VAL* 4.7 15.5 - - + +
444B TYR* 4.7 8.2 + - - -
447B TRP* 3.8 31.2 - - + +
449B TYR* 3.7 12.8 - - - +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 3.7 7.9 - - - -
260A PRO* 3.2 23.4 - - - +
261A PHE* 3.0 38.6 + - + +
262A TYR* 4.6 1.7 + - - -
52B ARG* 5.2 6.7 - - + +
53B ASP* 2.8 27.2 + - + +
55B ARG* 1.3 79.6 - - - +
57B ALA* 1.3 66.4 + - - +
58B GLN 3.2 2.7 - - - -
59B HIS* 2.8 23.9 + - - +
60B PHE* 3.5 22.9 + - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.4 13.5 - - + -
52B ARG* 6.0 0.8 - - - +
53B ASP 3.5 3.6 + - - -
54B PRO* 3.4 17.5 + - + +
56B ASP* 1.3 76.4 - - - +
58B GLN* 1.3 65.1 + - - +
60B PHE* 3.1 3.1 + - - +
61B THR* 2.8 29.9 + - + +
76B SER* 4.3 3.1 - - - +
80B VAL* 5.1 2.2 - - + -
477B ILE* 4.4 8.2 - - + +
480B PHE* 3.6 36.1 - - + -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.3 15.8 + - - -
54B PRO 4.6 1.2 + - - -
55B ARG 4.3 7.4 + - - +
56B ASP 3.0 1.4 + - - -
57B ALA* 1.3 78.3 - - - +
59B HIS* 1.3 77.0 + - + +
61B THR* 3.2 8.2 + - - -
62B GLN* 3.1 30.8 + - - +
73B ALA* 3.9 27.4 - - - +
76B SER* 3.8 7.9 - - - -
77B VAL* 3.5 14.8 - - + +
223B THR* 2.7 51.2 + - - +
224B VAL* 3.5 9.1 - - - +
225B VAL* 4.5 3.0 - - + +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A HIS* 3.5 22.5 - + - -
247A ILE* 4.3 22.5 - - + +
255A TRP* 3.4 5.6 - - + -
261A PHE* 3.7 39.3 - + + +
262A TYR* 2.8 31.7 + + - -
55B ARG 3.9 10.8 - - - -
56B ASP 2.8 15.5 + - - +
58B GLN* 1.3 87.0 + - + +
60B PHE* 1.3 64.6 + - - +
62B GLN* 3.9 4.5 + - - -
63B ARG* 3.3 35.6 + - - +
220B THR 5.8 0.6 + - - -
221B GLN* 4.7 9.1 - - + +
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.0 12.6 - - + +
121A ALA* 3.8 13.2 - - + -
255A TRP* 3.5 51.8 - + - -
259A SER* 4.8 1.6 - - - -
261A PHE* 4.1 15.0 - + - -
45B LEU* 3.8 14.2 - - + +
48B ILE* 3.7 32.1 - - + -
49B LEU* 3.5 25.4 - - + -
52B ARG* 3.6 23.8 - - - -
56B ASP* 3.6 23.3 - - + -
57B ALA 3.1 3.2 + - - +
59B HIS* 1.3 77.0 - - - +
61B THR* 1.3 63.9 + - - +
63B ARG* 3.2 20.3 + - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 4.5 8.3 - - + -
49B LEU* 3.8 26.9 - - + -
57B ALA 2.8 22.9 + - - +
58B GLN* 3.2 7.3 + - - -
60B PHE* 1.3 65.5 - - - +
62B GLN* 1.3 71.4 + - - +
63B ARG 3.0 2.2 - - - -
64B ALA* 2.9 22.9 + - - +
72B HIS* 3.3 12.7 + - - +
76B SER* 3.0 25.0 + - - +
468B HIS* 3.8 11.4 - - + -
480B PHE* 4.0 10.3 - - + -
482B LEU* 4.0 12.8 - - + -
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN* 3.1 15.5 + - - +
59B HIS* 4.0 10.2 + - - +
60B PHE 3.2 0.6 - - - -
61B THR* 1.3 84.7 + - - +
63B ARG* 1.3 71.2 + - - +
64B ALA 3.1 2.1 + - - -
65B CYS 3.1 23.0 + - - +
68B CYS 5.2 0.2 - - - +
70B TYR 2.9 30.2 + - - +
72B HIS* 3.8 11.6 - - + -
73B ALA* 3.7 23.2 - - + +
219B HIS* 3.4 14.5 - - - +
220B THR* 3.0 44.8 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A CYS* 3.2 7.2 - - - +
118A VAL* 4.0 11.8 - - + +
148A CYS* 3.0 39.8 + - - +
247A ILE* 4.3 18.8 - - - +
249A CYS* 4.8 3.4 - - - +
255A TRP* 3.7 18.9 - - + -
267A SF4 3.6 25.6 - - - -
43B ARG* 2.8 21.5 + - - -
45B LEU* 4.3 2.4 - - - +
59B HIS* 3.3 28.2 + - - +
60B PHE 3.2 11.2 + - - +
61B THR 3.0 1.4 - - - -
62B GLN* 1.3 94.9 - - - +
64B ALA* 1.3 61.7 + - - +
65B CYS 3.0 2.5 - - - +
216B LYS* 4.3 6.9 - - - +
219B HIS* 3.5 26.9 - - - +
220B THR 5.0 1.8 + - - -
221B GLN* 4.6 4.6 + - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.7 27.0 + - - +
45B LEU* 3.6 18.7 - - + +
61B THR 2.9 17.9 + - - +
63B ARG* 1.3 79.3 - - - +
65B CYS* 1.3 58.6 + - - +
72B HIS* 4.1 21.1 - - + +
482B LEU* 4.4 3.6 - - + -
532B ALA* 3.1 19.0 - - - +
533B CYS* 5.0 1.8 - - - -
536B HIS* 4.3 14.6 - - + -
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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