Contacts of the strand formed by residues 12 - 17 (chain M) in PDB entry 2DFS
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 ARG 12 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M TYR 5.3 0.7 - - - -
11M ALA* 1.3 80.1 - - - +
13M VAL* 1.3 66.7 + - - +
24M SER* 4.6 2.9 - - - +
25M ALA 3.2 13.5 - - - +
26M GLU* 4.3 19.7 - - + +
62M LEU* 3.9 4.5 - - - +
63M ARG* 2.9 63.2 + - + +
64M ASN 3.0 25.2 + - - -
65M PRO* 3.8 4.9 - - - +
66M ASP* 2.7 43.6 + - - -
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Residues in contact with VAL 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M TYR* 3.7 28.9 - - + -
12M ARG* 1.3 79.7 - - - +
14M TRP* 1.3 64.6 + - - +
15M ILE* 4.3 5.6 - - + -
24M SER* 3.6 6.6 + - - -
25M ALA* 2.9 50.4 + - + +
27M LEU* 3.8 14.1 - - + -
40M LEU* 4.2 14.1 - - + -
60M PRO* 3.9 25.6 - - + +
61M PRO 3.4 9.4 - - - +
62M LEU* 4.0 7.4 - - + -
63M ARG* 4.3 2.3 - - - +
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Residues in contact with TRP 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M VAL* 1.3 76.6 - - - +
15M ILE* 1.3 61.9 + - - +
20M GLU* 5.9 1.8 - - - -
22M TRP* 3.6 40.2 - - + -
23M LYS* 3.3 22.4 - - - -
24M SER* 4.0 14.1 - - - -
60M PRO* 3.5 7.8 - - - +
61M PRO* 2.9 39.9 + - + +
62M LEU 3.7 12.6 + - - -
63M ARG* 3.4 39.9 - - + +
64M ASN 5.1 0.4 - - - +
81M HIS* 4.9 0.2 - + - -
83M PRO* 3.6 31.6 - - + +
84M ALA* 4.6 4.6 - - - +
87M HIS* 3.4 50.9 - + + -
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Residues in contact with ILE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M VAL* 4.3 10.3 - - + -
14M TRP* 1.3 77.1 - - - +
16M PRO* 1.3 78.4 - - + +
22M TRP* 3.4 5.8 - - - -
23M LYS* 2.8 45.8 + - + +
25M ALA* 4.4 4.3 - - + -
40M LEU* 3.7 21.5 - - + -
42M LEU* 3.8 19.1 - - + -
48M LEU* 3.7 29.6 - - + -
50M TYR* 3.7 24.2 - - + -
60M PRO* 4.3 5.4 - - + -
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Residues in contact with PRO 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ILE* 1.3 97.3 - - + +
17M ASP* 1.3 59.7 + - - +
21M VAL 3.4 10.8 - - - +
22M TRP* 3.8 16.2 - - + -
50M TYR* 3.3 28.3 - - + +
60M PRO* 5.9 0.4 - - + -
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Residues in contact with ASP 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO* 1.3 77.5 - - - +
18M PRO* 1.3 74.9 - - - +
19M GLU* 3.2 11.6 + - - +
20M GLU* 2.7 25.5 + - - +
21M VAL* 3.0 28.7 + - - +
22M TRP 4.0 0.7 - - - +
23M LYS* 3.0 53.7 + - + +
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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