Contacts of the strand formed by residues 39 - 46 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D GLU 3.6 14.8 - - - -
36D GLN 2.5 26.5 + - - +
37D ASP* 3.1 4.9 - - - -
38D ASP* 1.3 87.8 + - + +
40D GLU* 1.3 71.7 + - - +
57D ILE 3.0 12.1 - - - +
58D ASN* 3.7 27.0 + - + -
59D VAL* 4.9 0.4 - - - -
65D CYS* 4.1 8.5 - - + -
67D ILE* 4.4 6.7 - - + -
98D LEU* 4.6 3.2 + - + +
99D ASP* 2.5 40.0 + - + +
101D VAL* 3.9 18.6 - - + -
112D ILE* 3.8 36.1 - - + -
195H MET* 3.7 28.9 - - + +
196H ALA* 4.2 2.8 + - - +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP 5.3 2.5 - - - +
39D TYR* 1.3 80.7 - - - +
41D VAL* 1.4 59.8 + - - +
56D GLY* 3.2 3.1 - - - -
57D ILE* 2.8 34.2 + - + +
59D VAL* 3.1 25.1 - - + +
67D ILE* 4.3 4.3 - - - +
190H PHE* 5.9 0.7 - - - -
195H MET* 4.5 0.4 - - - -
196H ALA* 3.3 26.5 - - + +
197H TYR 4.8 2.4 - - - +
198H GLN* 2.9 41.8 + - - +
199H LEU* 5.2 4.0 - - - +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C VAL* 3.4 30.5 - - + -
40D GLU* 1.4 71.3 - - - +
42D VAL* 1.3 61.9 + - - +
54D PHE* 3.6 37.0 - - + -
55D GLU 4.4 0.2 - - - +
56D GLY* 4.1 2.2 - - - -
67D ILE* 4.0 16.4 - - + -
69D ILE* 5.8 0.2 - - + -
192H ILE* 4.0 16.6 - - + -
195H MET* 4.4 6.3 - - + +
196H ALA 2.8 13.0 + - - +
197H TYR* 3.1 18.9 - - + +
198H GLN* 2.7 30.8 + - - +
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C THR* 5.2 3.8 - - - +
123C VAL* 4.4 11.4 - - - +
40D GLU 3.9 2.5 - - - +
41D VAL* 1.3 83.0 - - - +
43D ARG* 1.3 62.9 + - + +
55D GLU* 2.9 28.3 + - - +
56D GLY* 3.3 32.1 - - - +
57D ILE* 4.0 6.7 - - + +
198H GLN* 4.1 22.2 - - + -
199H LEU 6.0 0.4 - - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.7 18.9 - - - +
119C THR* 5.9 5.2 - - + -
123C VAL* 4.7 4.9 - - - -
41D VAL* 4.6 1.2 - - - +
42D VAL* 1.3 83.4 - - + +
44D LYS* 1.3 77.6 + - - +
45D VAL* 4.2 10.3 - - - -
54D PHE* 3.3 7.4 - - - -
55D GLU* 2.9 58.1 + - + +
203G ALA* 2.4 50.9 + - - +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ASP* 2.7 41.1 + - + +
122C LYS* 5.9 0.2 - - - -
123C VAL* 4.7 2.6 - - - +
160C HIS* 5.4 7.7 + - - -
601C AMP 5.7 3.0 + - - +
43D ARG* 1.3 88.3 - - - +
45D VAL* 1.3 64.4 + - - +
46D GLY 3.8 7.0 - - - +
47D ARG* 3.4 47.0 - - - +
52D GLU* 3.1 25.8 + - - +
53D VAL 3.8 7.2 - - - +
54D PHE* 3.4 30.6 - - + -
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 6.0 3.6 - - - +
43D ARG* 4.2 11.0 - - - -
44D LYS* 1.3 80.2 - - - +
46D GLY* 1.3 56.6 + - - +
53D VAL* 2.6 20.2 + - + +
54D PHE 4.4 0.7 - - - -
55D GLU* 3.8 35.4 - - + +
66D ILE* 4.9 6.3 - - + -
115D TYR* 5.9 1.3 - - + -
701D AMP 3.8 27.6 + - + +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 3.8 10.4 - - - +
45D VAL* 1.3 79.2 - - - +
47D ARG* 1.3 65.8 + - - +
52D GLU 3.7 0.2 - - - -
53D VAL* 2.7 37.2 + - - +
701D AMP 4.4 14.1 - - - -
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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