Contacts of the helix formed by residues 65 - 74 (chain F) in PDB entry 3J41
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 PHE 65 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F PHE 4.7 5.8 - - - -
13F LYS* 4.1 35.0 - - + -
16F PHE* 3.2 55.0 - + + -
17F SER* 5.3 3.8 - - - -
20F ASP* 5.6 1.3 - - + -
23F GLY 5.8 1.3 - - - -
25F GLY* 2.9 28.4 + - - +
64F ASP* 1.3 72.0 - - - +
66F PRO* 1.4 68.2 - - + +
68F PHE* 3.9 7.1 + - - +
69F LEU* 3.7 20.0 - - + +
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Residues in contact with PRO 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ASP* 3.6 10.8 - - + +
65F PHE* 1.4 93.0 - - + +
67F GLU* 1.3 60.1 + - + +
69F LEU* 2.9 28.0 + - + +
70F THR* 2.9 15.1 + - - -
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F VAL* 4.8 2.1 - - - +
56F ASP* 3.5 9.9 - - - -
57F ALA* 2.8 41.5 + - - +
58F ASP* 4.0 10.6 - - - +
63F ILE* 3.7 24.0 - - + +
64F ASP* 2.9 30.1 + - - +
66F PRO* 1.3 76.2 - - + +
68F PHE* 1.3 58.3 + - - +
70F THR* 3.0 32.3 + - - +
71F MET* 2.9 30.0 + - - +
76F MET 5.3 0.2 - - - +
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D ARG* 3.7 31.9 - - + -
15F ALA 3.5 25.1 - - - -
16F PHE* 3.6 38.1 - + + -
19F PHE* 5.3 11.0 - + + -
27F ILE* 3.7 31.4 - - + -
63F ILE* 3.4 18.6 - - + +
64F ASP 2.9 6.9 + - - +
65F PHE 3.9 2.0 - - - +
66F PRO 3.3 0.2 - - - -
67F GLU* 1.3 76.4 - - - +
69F LEU* 1.3 65.8 + - + +
71F MET* 3.3 5.1 + - - +
72F MET* 3.2 53.8 + - + +
146F THR* 5.8 1.3 - - + -
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.8 60.3 - - + +
15F ALA* 6.4 1.1 - - + -
16F PHE* 5.8 2.0 - - + -
65F PHE* 3.7 18.8 - - + +
66F PRO* 2.9 13.2 + - + +
68F PHE* 1.3 85.7 - - + +
70F THR* 1.3 59.0 + - - +
72F MET* 3.2 6.7 + - + +
73F ALA* 2.9 38.5 + - + +
74F ARG* 5.2 2.2 - - - -
146F THR* 6.0 2.5 - - + -
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Residues in contact with THR 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F VAL* 5.1 1.1 - - + -
57F ALA* 5.1 4.0 - - + -
66F PRO 2.9 13.6 + - - -
67F GLU* 3.0 32.2 + - - +
69F LEU* 1.3 73.1 - - - +
71F MET* 1.3 57.0 + - - +
74F ARG* 2.9 33.6 + - + +
75F LYS 2.8 26.7 + - - -
76F MET 3.8 20.9 - - - +
78F ASP 5.2 2.9 - - - +
79F THR* 4.8 8.7 - - - +
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LYS* 6.0 0.2 - - - +
234D LEU* 4.9 12.6 - - + -
237D LEU* 6.0 3.6 - - + -
51F MET 4.0 21.1 - - - +
52F ILE* 4.1 21.5 - - + -
55F VAL* 4.0 34.2 - - + +
56F ASP* 5.8 0.7 - - - -
63F ILE* 4.3 27.4 - - + -
67F GLU* 2.9 20.3 + - - +
68F PHE* 3.3 11.4 + - - +
70F THR* 1.3 75.3 - - - +
72F MET* 1.3 78.7 + - + +
75F LYS* 4.1 16.3 - - - +
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Residues in contact with MET 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 6.0 4.9 - - + -
241D ARG* 4.0 22.7 - - + +
12F PHE* 6.5 0.4 - - + -
68F PHE* 3.2 47.1 + - + +
69F LEU* 3.2 9.1 + - + +
71F MET* 1.3 102.3 - - + +
73F ALA* 1.3 60.7 + - + +
74F ARG 4.0 0.2 - - - -
75F LYS* 5.0 3.8 - - - +
85F ILE* 6.0 0.9 - - - +
141F PHE* 5.4 6.2 - - - -
142F VAL* 3.8 23.2 - - + +
145F MET* 3.8 35.1 - - + +
146F THR* 3.9 14.8 - - + +
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Residues in contact with ALA 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 5.7 5.6 - - + -
69F LEU* 2.9 17.4 + - + +
72F MET* 1.3 78.3 - - + +
74F ARG* 1.3 66.7 - - - +
75F LYS* 5.3 0.2 - - - -
82F GLU* 4.0 6.9 - - - +
85F ILE* 3.9 13.6 - - - +
138F TYR* 3.6 21.4 + - - +
142F VAL* 4.1 24.3 - - + +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU 4.8 1.1 - - - -
70F THR* 2.9 34.0 + - + +
73F ALA* 1.3 82.5 - - - +
75F LYS* 1.3 67.1 + - - +
76F MET* 3.1 3.5 + - - +
78F ASP 4.7 0.9 - - - +
79F THR 2.8 26.4 + - - +
80F ASP* 2.7 33.6 + - - +
81F SER* 3.1 48.3 - - - +
82F GLU* 2.7 38.6 + - + +
84F GLU* 5.5 0.2 - - - +
85F ILE* 3.8 5.0 + - - +
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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