Contacts of the strand formed by residues 41 - 48 (chain D) in PDB entry 5DPR
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 LYS 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ILE* 5.4 0.7 - - - +
35D ARG* 4.2 10.0 + - - +
38D HIS* 3.1 28.6 + - + +
39D PRO 3.2 2.2 - - - +
40D SER* 1.3 96.8 + - - +
42D ILE* 1.3 68.6 + - - +
43D PRO* 4.0 5.5 - - - +
64D LEU* 3.5 47.2 + - + +
65D VAL 3.2 10.8 - - - +
66D PRO* 3.9 24.8 - - + +
67D ASP* 4.1 0.4 - - - -
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Residues in contact with ILE 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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35D ARG* 4.0 11.4 - - - +
41D LYS* 1.3 76.5 - - - +
43D PRO* 1.4 67.4 - - + +
44D VAL* 3.4 20.6 + - + +
63D PHE 3.5 0.9 - - - +
64D LEU* 3.7 2.5 - - - -
65D VAL 2.5 35.8 + - - +
67D ASP* 3.2 24.0 - - - +
106D ILE* 3.9 28.0 - - + -
107D ALA* 4.0 11.9 - - + -
110D TYR* 3.4 52.0 - - + -
120D LEU* 4.3 7.0 - - + -
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Residues in contact with PRO 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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31D VAL* 4.3 16.8 - - + -
34D ILE* 4.2 18.8 - - + -
35D ARG* 4.4 11.2 - - + -
41D LYS 4.0 6.3 - - - +
42D ILE* 1.4 85.2 - - + +
44D VAL* 1.3 59.4 + - - +
63D PHE 3.9 3.8 - - - +
64D LEU* 4.1 5.4 - - + -
110D TYR* 4.0 12.3 - - + +
118D GLY 4.1 15.5 - - - +
119D PHE* 3.7 23.3 - - + -
120D LEU* 3.0 25.8 + - - +
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Residues in contact with VAL 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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42D ILE* 3.8 15.0 - - + +
43D PRO* 1.3 79.0 - - - +
45D ILE* 1.3 66.8 + - - +
46D ILE* 3.6 25.8 - - + -
61D THR 3.7 0.7 - - - +
62D LYS* 3.6 3.1 - - - +
63D PHE* 2.8 45.3 + - + +
65D VAL* 3.8 11.7 - - + -
74D LEU* 5.1 0.2 - - + -
106D ILE* 3.7 29.4 - - + -
119D PHE* 4.5 0.8 - - - -
120D LEU* 3.3 14.8 - - + +
122D MET* 3.8 22.4 - - + -
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Residues in contact with ILE 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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18D PHE* 3.6 39.7 - - + -
44D VAL* 1.3 75.5 - - - +
46D ILE* 1.3 60.3 + - - +
47D GLU* 3.9 9.2 - - + -
61D THR* 3.6 17.3 - - + +
62D LYS* 4.0 19.1 - - + -
119D PHE* 3.5 38.6 - - + -
120D LEU 2.7 9.7 + - - +
121D TYR* 3.5 29.8 - - + -
122D MET* 2.7 33.1 + - - +
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Residues in contact with ILE 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 VAL* 3.6 21.3 - - + -
45D ILE* 1.3 77.0 - - - +
47D GLU* 1.3 65.8 + - - +
58D LEU* 3.9 13.9 - - + +
60D LYS 4.1 4.9 - - - +
61D THR* 3.0 26.0 + - - +
63D PHE* 3.8 26.7 - - + -
74D LEU* 4.7 6.7 - - + -
78D ILE* 3.6 31.9 - - + -
92D LEU* 4.0 15.7 - - + -
122D MET* 3.5 16.8 - - + +
124D TYR* 3.9 22.0 - - + -
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Residues in contact with GLU 47 (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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14D SER 4.8 4.0 - - - +
16D ARG 4.0 0.9 - - - +
17D PRO* 3.5 13.4 - - - +
18D PHE* 2.8 38.2 + - - +
19D LYS 5.2 0.2 + - - -
21D ARG* 3.5 13.4 + - - +
45D ILE* 3.9 15.0 - - + +
46D ILE* 1.3 79.7 - - - +
48D ARG* 1.3 66.3 + - - +
58D LEU* 6.2 0.2 - - - -
61D THR* 4.1 4.9 - - + -
121D TYR* 4.7 8.5 - - - -
122D MET 3.1 8.9 + - - +
123D VAL* 3.3 12.6 - - + +
124D TYR* 3.1 31.6 + - - -
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Residues in contact with ARG 48 (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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47D GLU* 1.3 80.4 - - - +
49D TYR* 1.3 74.5 + - - +
50D LYS* 3.6 1.6 + - - -
52D GLU* 3.4 35.8 + - + -
53D LYS* 4.2 9.7 + - - +
55D LEU 2.5 37.5 + - - -
56D PRO* 3.9 12.0 - - - +
57D VAL* 3.4 33.7 - - + +
123D VAL* 4.1 1.9 - - - +
124D TYR* 3.5 30.4 - - + +
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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