Contacts of the strand formed by residues 39 - 46 (chain A) in PDB entry 1DS5
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 TYR 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU 3.8 6.1 - - - -
36A GLN* 2.4 36.3 + - - +
37A ASP* 3.0 7.5 - - - -
38A ASP* 1.3 88.1 - - + +
40A GLU* 1.3 70.8 + - - +
57A ILE 3.0 17.5 - - - +
58A ASN* 4.1 20.7 + - + -
59A VAL* 4.7 1.6 - - - +
65A CYS* 3.9 16.6 - - + -
67A ILE* 4.5 3.8 - - + -
98A LEU* 5.2 1.4 - - - +
99A ASP* 3.2 34.9 + - - +
101A VAL* 4.7 6.1 - - + -
112A ILE* 3.4 39.3 - - + +
195F MET* 4.3 21.9 - - + +
196F ALA* 4.1 12.5 + - - +
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Residues in contact with GLU 40 (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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37A ASP 5.9 0.7 - - - +
39A TYR* 1.3 83.1 - - - +
41A VAL* 1.3 64.8 + - - +
56A GLY* 3.1 3.3 - - - -
57A ILE* 2.7 44.9 + - + +
59A VAL* 4.3 16.4 - - + +
67A ILE* 4.3 2.7 - - - +
195F MET* 5.2 0.2 - - - -
196F ALA* 3.3 22.5 - - + +
197F TYR* 4.7 1.1 - - - -
198F GLN* 3.0 45.3 + - + +
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Residues in contact with VAL 41 (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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40A GLU* 1.3 74.1 - - - +
42A VAL* 1.4 62.2 + - - +
54A PHE* 3.6 37.7 - - + -
55A GLU 4.7 0.2 - - - +
56A GLY* 4.1 2.5 - - - -
67A ILE* 3.9 17.9 - - + -
69A ILE* 5.4 0.7 - - + -
123B VAL* 3.9 16.1 - - + +
192F ILE* 3.7 21.5 - - + -
195F MET* 4.5 8.2 - - + +
196F ALA 3.0 10.5 + - - +
197F TYR* 2.8 58.3 - - + +
198F GLN* 3.7 6.1 + - - +
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Residues in contact with VAL 42 (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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40A GLU 4.5 6.7 - - - +
41A VAL* 1.4 77.3 - - - +
43A ARG* 1.3 83.4 + - - +
55A GLU* 3.0 20.8 + - - +
56A GLY* 4.5 8.3 - - - -
57A ILE* 4.7 7.6 - - + -
119B THR* 5.9 1.9 - - - +
123B VAL* 4.1 12.0 - - - +
198F GLN* 4.4 14.4 - - + +
199F LEU 3.7 15.4 - - - +
200F GLN* 5.4 0.2 - - - -
201F LEU* 3.4 40.3 + - + +
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Residues in contact with ARG 43 (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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42A VAL* 1.3 88.2 - - - +
44A LYS* 1.3 73.0 + - - +
45A VAL* 4.5 7.4 - - + -
54A PHE* 3.3 8.2 - - - -
55A GLU* 2.9 70.4 + - + +
64A LYS* 5.5 2.4 - - - +
119B THR* 6.5 0.9 - - - -
123B VAL* 4.9 4.2 - - - +
201F LEU* 3.2 51.1 + - - +
202F GLN* 6.0 0.4 - - - +
203F ALA* 2.8 28.5 + - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 1.3 76.6 - - - +
45A VAL* 1.3 87.5 + - - +
46A GLY 3.7 7.6 - - - +
47A ARG* 3.0 40.5 - - + +
52A GLU* 2.4 37.1 + - - -
53A VAL 3.4 9.9 - - - +
54A PHE* 3.5 26.8 - - + -
120B ASP* 2.9 39.6 + - + +
121B PHE* 5.1 3.0 - - - -
122B LYS* 3.0 26.0 - - - +
123B VAL* 4.8 3.6 - - - +
160B HIS* 5.4 2.6 + - - -
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Residues in contact with VAL 45 (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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43A ARG* 3.6 18.4 + - + +
44A LYS* 1.3 84.2 - - - +
46A GLY* 1.3 56.5 + - - +
47A ARG* 6.1 1.6 - - - -
53A VAL* 2.7 24.2 + - + +
55A GLU* 4.8 13.0 - - + +
66A ILE* 5.0 4.0 - - + -
115A TYR* 6.4 0.9 - - + -
501A AMP 3.5 40.0 + - + +
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Residues in contact with GLY 46 (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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44A LYS* 3.7 5.0 - - - +
45A VAL* 1.3 80.3 - - - +
47A ARG* 1.3 67.3 + - - +
48A GLY 4.2 0.2 - - - -
52A GLU 3.6 0.2 - - - -
53A VAL* 2.6 38.4 + - - +
501A AMP 3.7 21.8 - - - -
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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