Contacts of the helix formed by residues 58 - 69 (chain A) in PDB entry 3RFM
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 LEU 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 2.6 23.2 + - + +
57A VAL* 1.3 95.4 - - + +
59A ALA* 1.3 55.5 + - - +
61A PRO* 3.0 8.4 - - + +
62A PHE* 2.7 65.5 + - + -
79A PHE* 5.7 2.9 - - + -
83A PHE* 3.5 31.9 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 3.0 4.6 + - - -
55A VAL* 3.4 28.3 - - + +
58A LEU* 1.3 77.6 - - - +
60A ILE* 1.3 57.3 + - - +
62A PHE* 3.3 4.7 + - - +
63A ALA* 2.8 30.0 + - - +
83A PHE* 3.9 11.8 - - + -
84A VAL* 4.8 20.4 - - + +
87A LEU* 3.6 16.2 - - + -
278A HIS* 4.7 4.8 - - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 3.4 37.7 - - - +
14A LEU* 5.5 0.2 - - + -
16A ILE* 3.7 17.5 - - + -
17A ALA* 3.6 37.0 - - + +
20A ALA* 5.3 0.2 - - + -
55A VAL* 2.6 32.9 + - + +
56A GLY* 3.9 7.4 - - - -
59A ALA* 1.3 69.7 - - - +
61A PRO* 1.3 73.2 - - + +
63A ALA* 2.9 8.0 + - - +
64A ILE* 2.9 41.2 + - + +
278A HIS* 4.1 11.0 - - + -
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 5.5 0.7 - - + -
55A VAL 3.7 1.8 - - - +
56A GLY 4.1 7.2 - - - +
57A VAL 3.0 23.6 - - - +
58A LEU* 3.0 19.7 - - + +
60A ILE* 1.3 96.7 - - + +
62A PHE* 1.3 62.6 + - + +
64A ILE* 3.3 11.2 + - + +
65A THR* 2.9 29.1 + - - -
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 2.7 61.2 + - + +
59A ALA* 3.5 4.5 - - - +
61A PRO* 1.3 75.1 - - + +
63A ALA* 1.3 58.2 + - - +
65A THR* 3.1 6.6 + - - -
66A ILE* 2.9 34.7 + - - +
79A PHE* 3.9 22.7 - + - -
80A ILE* 3.4 54.0 - - + +
83A PHE* 3.9 27.4 - + + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.5 10.2 + - - +
13A GLU* 5.6 0.4 - - - +
59A ALA 2.8 18.1 + - - +
60A ILE* 2.9 6.3 + - + +
62A PHE* 1.3 77.1 - - - +
64A ILE* 1.3 61.3 + - + +
66A ILE* 3.4 11.2 - - - +
67A SER* 3.2 24.9 + - - -
84A VAL* 6.6 0.2 - - + -
278A HIS* 3.8 28.3 - - + +
330A CFF 4.4 15.3 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.8 7.0 - - + -
10A ILE* 4.4 28.5 - - + +
13A GLU* 3.6 30.5 - - + -
14A LEU* 3.5 30.7 - - + -
60A ILE* 2.9 30.5 + - + +
61A PRO* 3.7 9.0 - - + +
62A PHE 3.2 0.2 - - - -
63A ALA* 1.3 77.2 - - - +
65A THR* 1.3 58.2 + - - +
67A SER* 2.7 21.6 + - - +
68A THR* 4.2 7.1 + - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PRO 2.9 14.7 + - - -
62A PHE* 3.6 10.7 - - - -
64A ILE* 1.3 76.4 - - - +
66A ILE* 1.3 63.9 + - - +
67A SER 3.1 1.6 - - - -
68A THR* 3.1 20.5 + - - +
69A GLY* 3.3 7.1 + - - +
70A PHE* 3.7 29.3 - - + -
80A ILE* 5.4 5.6 - - + -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE 2.9 20.4 + - - +
63A ALA* 3.4 15.9 - - - +
65A THR* 1.3 74.1 - - - +
67A SER* 1.3 68.1 + - - +
69A GLY* 3.2 12.7 + - - +
70A PHE* 4.3 11.9 - - + -
80A ILE* 4.7 5.4 - - + +
81A ALA* 3.5 35.4 - - + +
166A CYS* 3.7 25.0 - - - +
167A LEU* 4.8 4.3 - - - +
168A PHE* 3.6 33.5 + - + +
330A CFF 4.7 13.2 - - - +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.6 16.9 - - - -
63A ALA 3.2 16.7 + - - -
64A ILE* 2.7 25.8 + - - +
66A ILE* 1.3 81.4 - - - +
68A THR* 1.3 66.3 + - - +
167A LEU* 5.9 0.7 - - - +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 6.6 0.2 - - + -
64A ILE 4.4 5.3 + - - +
65A THR* 3.1 13.2 + - - +
67A SER* 1.3 90.5 + - - +
69A GLY* 1.3 68.2 + - - +
167A LEU* 4.8 3.3 - - - +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR 3.3 4.1 + - - +
66A ILE 3.2 9.1 + - - -
68A THR* 1.3 91.0 + - - +
70A PHE* 1.3 66.0 + - - +
166A CYS 3.6 5.8 - - - -
167A LEU* 3.6 25.8 - - - -
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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