Contacts of the helix formed by residues 13 - 21 (chain F) in PDB entry 3DOY
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 13 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 5.5 4.3 - - - -
115B PRO 5.7 0.2 - - - -
11F GLN* 3.8 38.1 - - + -
12F PHE* 1.3 75.0 - - - +
14F ILE* 1.3 71.0 + - + +
15F GLU* 3.1 18.6 - - + +
16F HIS* 2.8 37.6 + + - +
17F ILE* 3.0 13.4 + - - +
31F ASP 4.2 0.9 - - - -
32F ARG* 3.4 47.6 - - - -
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Residues in contact with ILE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.6 46.2 - - + -
63B PRO* 4.1 20.2 - - + +
114B THR* 5.2 5.2 - - + +
115B PRO* 4.2 25.0 + - + +
13F PHE* 1.3 72.2 - - + +
15F GLU* 1.3 65.1 + - + +
17F ILE* 3.2 7.3 + - + +
18F LEU* 2.8 36.4 + - + +
28F LEU* 3.9 14.8 - - + -
30F VAL 3.9 18.6 - - - +
31F ASP* 3.5 18.7 + - - +
32F ARG* 5.6 0.2 - - - +
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Residues in contact with GLU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN 5.6 6.1 - - - +
63B PRO* 5.7 4.5 - - + -
13F PHE* 4.1 19.5 - - + +
14F ILE* 1.3 81.6 - - + +
16F HIS* 1.3 86.0 + - + +
18F LEU* 3.5 13.0 + - - +
19F GLN* 3.4 26.4 + - - +
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Residues in contact with HIS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLN 4.4 4.7 - - - -
12F PHE* 3.4 22.4 - + + -
13F PHE* 2.8 45.8 + + - +
15F GLU* 1.3 93.1 + - - +
17F ILE* 1.3 67.8 + - - +
19F GLN* 3.0 20.0 + - - +
20F ILE* 3.3 9.0 + - - +
80F PHE* 4.8 0.9 - - - -
89F PHE* 3.7 39.4 - + + -
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Residues in contact with ILE 17 (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 4.4 1.8 - - - +
13F PHE 3.0 15.1 + - - +
14F ILE* 3.5 8.3 - - - +
16F HIS* 1.3 76.4 - - - +
18F LEU* 1.3 58.4 + - - +
20F ILE 3.2 1.2 + - - -
21F LEU* 2.9 55.3 + - + +
28F LEU* 4.1 13.0 - - + -
30F VAL* 3.6 21.5 - - + +
31F ASP 3.5 35.4 - - - +
32F ARG* 3.5 15.7 - - - +
33F ILE* 4.0 20.2 - - + -
80F PHE* 4.2 11.2 - - + -
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.0 17.0 - - + -
61B ASN* 5.0 13.9 - - - +
63B PRO* 4.4 12.1 - - + -
14F ILE* 2.8 36.9 + - + +
15F GLU* 3.6 11.0 - - - +
16F HIS 3.1 0.2 - - - -
17F ILE* 1.3 77.0 - - - +
19F GLN* 1.3 60.9 + - + +
21F LEU 3.4 7.7 - - - +
24F ARG* 3.0 53.7 + - - +
28F LEU* 3.5 27.6 - - + -
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Residues in contact with GLN 19 (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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15F GLU* 3.4 15.1 + - - +
16F HIS* 3.0 15.7 + - - +
18F LEU* 1.3 78.4 - - + +
20F ILE* 1.3 60.2 + - - +
89F PHE* 3.3 23.8 - - + -
91F PRO* 3.5 41.2 - - + +
94F ALA* 3.5 15.8 - - - +
95F LYS* 5.0 1.2 + - - +
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Residues in contact with ILE 20 (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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16F HIS 3.3 2.2 + - - +
17F ILE 3.2 2.4 + - - +
19F GLN* 1.3 86.3 - - - +
21F LEU* 1.3 66.6 + - + +
22F PRO* 3.7 5.4 - - - +
80F PHE* 3.9 26.2 - - + -
83F PHE* 3.5 43.9 - - + -
84F THR* 4.7 3.6 - - + -
88F GLY 4.9 2.5 - - - +
89F PHE* 3.5 35.7 - - + -
90F ASP 3.9 36.6 - - - +
91F PRO* 4.1 1.8 - - + -
94F ALA* 3.5 18.5 - - + +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ILE* 2.9 35.8 + - + +
18F LEU 3.4 8.8 - - - +
20F ILE* 1.3 74.2 - - - +
22F PRO* 1.3 67.8 - - + +
23F HIS* 3.3 13.2 - - + +
24F ARG* 2.9 20.4 + - - -
28F LEU* 4.0 14.8 - - + -
30F VAL* 4.7 5.8 - - + -
76F GLN* 3.9 34.3 - - + +
79F GLY* 4.1 5.4 - - - -
80F PHE* 3.7 38.6 - - + +
83F PHE* 4.2 12.8 - - + -
99F VAL* 5.6 0.4 - - + -
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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