Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 2DMM
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 ILE 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.5 15.3 - - + +
49A LEU* 5.7 2.7 - - + +
74A LEU* 3.8 37.1 - - + +
77A ASP* 2.8 53.1 + - - +
79A ASN* 1.3 80.3 - - + +
81A VAL* 1.3 71.2 + - - +
82A ILE* 4.2 8.5 - - + -
106A PHE* 5.6 3.1 - - + -
131A LEU* 4.1 21.5 - - + +
135A ALA* 3.4 33.0 - - + -
138A GLY* 4.8 6.7 - - - +
139A PRO* 5.2 1.8 - - + -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 4.7 17.0 - - + -
40A ILE* 5.0 7.4 - - + -
46A LYS* 3.4 37.0 - - + +
47A ASP 3.1 6.7 + - - -
48A VAL* 3.3 22.3 - - + +
49A LEU 3.1 22.0 + - - -
77A ASP 5.2 1.3 - - - +
78A PRO 5.6 2.9 - - - +
79A ASN 4.6 2.0 - - - +
80A ILE* 1.3 80.2 - - - +
82A ILE* 1.3 73.2 + - - +
83A ALA* 5.1 0.4 - - + -
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO 4.3 2.3 - - - +
29A VAL* 3.8 8.5 - - + -
30A LYS* 3.1 21.5 + - - +
49A LEU* 3.5 34.5 - - + -
67A TYR* 3.4 31.6 - - + +
70A LEU* 3.8 5.4 - - + +
71A GLY* 3.7 32.5 + - - +
74A LEU* 3.3 37.7 - - + +
80A ILE* 4.2 4.7 - - + -
81A VAL* 1.3 77.9 - - - +
83A ALA* 1.3 64.1 + - - +
131A LEU* 4.2 0.9 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.3 9.0 - - - -
30A LYS* 3.0 24.0 - - + +
32A VAL* 3.2 24.2 - - + -
40A ILE* 4.9 2.5 - - + -
48A VAL* 4.8 11.2 - - + -
49A LEU 3.0 22.2 + - - +
50A ILE* 4.5 3.6 - - + -
51A GLU 3.2 11.8 + - - -
67A TYR* 3.2 8.8 + - - -
81A VAL* 4.8 0.9 - - + +
82A ILE* 1.3 76.8 - - - +
84A LYS* 1.3 57.3 + - - +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.5 29.2 - - + -
30A LYS 2.8 9.7 + - - +
31A VAL* 3.7 29.9 - - + +
32A VAL* 2.8 28.8 + - - +
50A ILE* 4.2 2.9 - - - -
51A GLU* 3.5 19.7 - - - +
53A TYR* 3.5 35.9 + - + -
64A GLU* 5.8 3.4 + - - -
67A TYR* 4.6 3.8 - - + -
83A ALA* 1.3 75.2 - - - +
85A MET* 1.3 59.7 + - - +
86A ASP* 4.9 1.9 + - - +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 6.0 0.2 - - - -
32A VAL 2.8 24.9 - - - +
33A VAL* 4.4 2.5 - - - -
34A ALA 4.7 5.4 - - - +
37A PHE* 4.8 6.3 - - + -
50A ILE* 3.5 20.1 - - + +
51A GLU 3.2 7.0 + - - -
52A PHE* 3.2 40.3 - - + -
53A TYR* 3.5 4.1 + - - -
84A LYS* 1.3 74.5 - - - +
86A ASP* 1.3 61.8 + - - +
87A ALA* 3.2 19.4 + - - -
90A ASN* 2.8 46.7 - - + +
91A ASP 3.3 15.3 - - - +
92A VAL* 3.6 15.7 - - + -
93A PRO* 4.5 5.8 - - + -
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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