Contacts of the helix formed by residues 13 - 21 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN* 3.8 37.5 - - + -
12B PHE* 1.3 74.8 - - - +
14B ILE* 1.3 69.8 + - + +
15B GLU* 3.2 20.2 - - - +
16B HIS* 2.9 35.0 + + + +
17B ILE* 3.1 10.5 + - - +
31B ASP 4.1 2.2 - - - -
32B ARG* 3.4 47.3 - - - -
114F THR* 5.9 1.1 - - - -
115F PRO 6.1 0.4 - - - +
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 1.3 71.1 - - + +
15B GLU* 1.3 72.0 + - + +
17B ILE* 3.1 6.6 + - + +
18B LEU* 2.8 36.1 + - + +
28B LEU* 4.0 13.2 - - + -
30B VAL 3.9 20.0 - - - +
31B ASP* 3.4 16.5 + - - +
32B ARG* 5.7 0.2 - - - +
50F PHE* 3.7 45.5 - - + -
63F PRO* 4.1 17.5 - - + +
114F THR* 5.2 4.5 - - - +
115F PRO* 4.1 24.3 + - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.3 22.9 - - - +
14B ILE* 1.3 90.2 - - + +
16B HIS* 1.3 75.6 + - + +
18B LEU* 3.3 13.7 + - + +
19B GLN* 3.2 30.6 + - - +
61F ASN 5.4 6.3 - - - +
62F LYS* 5.9 9.0 - - + +
63F PRO* 5.1 8.7 - - + -
114F THR* 6.0 0.7 - - - -
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Residues in contact with HIS 16 (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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11B GLN 4.7 2.5 + - - -
12B PHE* 3.8 24.8 - + + -
13B PHE* 2.9 46.3 + + + +
15B GLU* 1.3 87.8 + - + +
17B ILE* 1.3 65.5 + - - +
19B GLN* 3.0 13.4 + - - -
20B ILE* 3.3 10.4 + - - +
80B PHE* 5.0 0.4 - - - -
89B PHE* 3.5 44.2 - + + -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.2 2.7 - - + +
13B PHE 3.1 11.7 + - - +
14B ILE* 3.4 8.3 - - + +
16B HIS* 1.3 75.9 - - - +
18B LEU* 1.3 57.9 + - - +
20B ILE 3.1 1.6 + - - -
21B LEU* 2.9 43.9 + - + +
28B LEU* 3.9 29.8 - - + -
30B VAL* 3.6 20.2 - - + +
31B ASP 3.5 35.7 - - - +
32B ARG* 3.6 13.5 - - - +
33B ILE* 4.0 20.4 - - + -
80B PHE* 4.2 9.4 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 2.8 36.8 + - + +
15B GLU* 3.6 13.2 - - - +
16B HIS 3.2 0.4 - - - -
17B ILE* 1.3 72.0 - - - +
19B GLN* 1.3 60.6 + - + +
21B LEU 3.4 6.2 - - - +
24B ARG* 2.8 58.8 + - - +
28B LEU* 3.5 25.8 - - + -
50F PHE* 4.0 12.3 - - + -
61F ASN* 5.0 14.4 - - - +
63F PRO* 4.3 19.1 - - + -
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Residues in contact with GLN 19 (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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15B GLU* 3.2 16.6 + - - +
16B HIS* 3.0 12.9 + - - +
18B LEU* 1.3 78.6 - - + +
20B ILE* 1.3 61.6 + - - +
89B PHE* 3.4 19.7 - - + -
91B PRO* 3.6 43.4 - - + +
94B ALA* 3.7 14.6 - - - +
95B LYS* 5.6 2.8 - - - +
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Residues in contact with ILE 20 (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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16B HIS 3.6 12.3 - - - +
17B ILE 3.1 1.6 + - - +
19B GLN* 1.3 86.9 - - - +
21B LEU* 1.3 65.6 + - + +
22B PRO* 3.8 1.4 - - - +
80B PHE* 3.5 36.1 - - + -
83B PHE* 3.6 35.0 - - + -
84B THR* 4.6 2.5 - - + -
89B PHE* 3.7 29.6 - - + -
90B ASP 4.0 24.7 - - - +
91B PRO 4.2 0.7 - - - -
94B ALA* 3.8 7.6 - - + +
158B ARG* 5.1 0.9 + - - -
2009B BEN 3.5 26.3 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 2.9 26.2 + - + +
18B LEU* 3.4 9.1 - - - +
20B ILE* 1.3 74.0 - - - +
22B PRO* 1.3 64.3 - - + +
23B HIS* 3.9 11.2 - - + +
24B ARG* 2.9 21.5 + - - -
28B LEU* 3.8 27.1 - - + -
30B VAL* 4.6 5.6 - - + -
76B GLN* 4.0 38.6 - - + +
80B PHE* 4.2 20.4 - - + +
2009B BEN 3.7 35.2 - - + +
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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
------------------------------------------------------------
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