Contacts of the strand formed by residues 21 - 26 (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 VAL 21 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO* 3.4 8.3 - - - +
17M ASP* 3.0 34.2 + - - +
18M PRO 4.6 0.6 - - - -
19M GLU 3.7 0.8 - - - -
20M GLU* 1.4 78.4 - - - +
22M TRP* 1.3 80.2 + - + +
82M GLU* 4.6 4.7 - - - +
86M LEU* 4.6 3.4 - - + -
675M GLU* 3.7 9.0 - - + +
676M LYS* 3.6 42.6 - - + +
679M VAL* 4.2 17.9 - - + -
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Residues in contact with TRP 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 3.6 50.0 - - + -
15M ILE 3.4 22.4 - - - -
16M PRO* 3.8 21.5 - - + -
17M ASP* 4.2 2.2 - - - -
20M GLU* 2.9 26.8 + - - +
21M VAL* 1.3 92.6 - - + +
23M LYS* 1.3 60.9 + - - +
60M PRO* 5.8 0.2 - - + -
61M PRO* 3.8 21.3 - - + -
82M GLU* 2.9 33.6 + - + +
83M PRO* 3.7 31.2 - - + +
86M LEU* 4.2 13.7 - - + -
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 3.3 7.7 - - - -
15M ILE* 2.8 43.4 + - + +
17M ASP* 3.0 46.0 + - + +
19M GLU* 4.8 8.5 - - - +
20M GLU* 5.2 6.3 - - + +
22M TRP* 1.3 73.8 - - - +
24M SER* 1.3 70.7 + - - +
42M LEU* 5.2 17.3 - - + -
43M GLU* 2.6 39.3 + - + +
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Residues in contact with SER 24 (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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12M ARG* 4.6 3.8 - - - +
13M VAL 3.6 5.8 + - - -
14M TRP* 4.0 11.7 - - - -
23M LYS* 1.3 80.5 - - - +
25M ALA* 1.3 65.3 + - - +
41M ARG 3.8 6.9 - - - +
42M LEU* 4.2 15.0 - - - +
43M GLU 5.1 0.2 + - - -
63M ARG* 2.8 39.8 + - - -
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Residues in contact with ALA 25 (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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12M ARG* 3.2 7.7 - - - +
13M VAL* 2.9 42.5 + - + +
15M ILE* 4.4 7.9 - - + -
24M SER* 1.3 77.4 + - - +
26M GLU* 1.3 60.3 + - - +
40M LEU* 3.7 32.5 - - + -
41M ARG 3.2 12.1 - - - +
42M LEU* 4.4 7.4 - - + -
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Residues in contact with GLU 26 (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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10M TYR* 3.5 39.1 - - - +
11M ALA 3.4 16.2 - - - +
12M ARG* 4.3 14.5 - - + +
25M ALA* 1.3 75.3 - - - +
27M LEU* 1.3 66.3 + - - +
28M LEU* 3.3 4.5 + - - +
40M LEU* 3.3 21.6 - - - -
41M ARG* 2.6 60.0 + - + +
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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