Contacts of the strand formed by residues 47 - 53 (chain D) in PDB entry 3Q3G
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 LEU 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C TYR* 5.5 0.7 - - + -
50C PRO* 3.7 35.4 - - + -
93C TYR* 3.8 33.6 - - + -
104C PHE* 3.6 37.9 - - + +
105C GLY 5.0 0.6 + - - -
609C EDO 3.1 28.2 + - - -
39D VAL* 3.8 20.4 - - + -
40D LYS 3.6 1.6 - - - -
41D GLN* 3.5 34.8 - - + +
46D GLY* 1.3 70.5 - - - -
48D GLU* 1.3 58.4 + - - +
97D TYR* 4.5 4.9 - - + -
114D TRP* 4.3 2.7 - - + -
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Residues in contact with GLU 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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609C EDO 4.3 15.5 - - - -
39D VAL* 3.7 3.4 - - - +
40D LYS* 2.7 53.7 + - + +
42D ARG* 3.6 22.6 + - - +
46D GLY 4.6 2.9 - - - +
47D LEU* 1.3 74.1 - - - +
49D TRP* 1.3 63.8 + - - +
50D ILE* 3.5 1.2 + - - +
63D ASP* 6.1 0.9 - - - +
65D LYS* 4.7 11.4 - - + +
66D PHE* 3.4 21.9 - - + -
705D GOL 3.1 32.6 + - - -
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Residues in contact with TRP 49 (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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100C TYR* 3.4 34.3 - + + -
101C PRO* 3.6 28.7 - - + -
102C LEU* 3.3 36.2 + - + +
104C PHE* 4.4 11.2 - - + -
609C EDO 4.8 2.4 + - - -
37D GLN* 2.7 25.0 + - + -
38D TRP 3.9 12.6 - - - -
39D VAL* 4.4 8.4 - - + +
47D LEU 4.2 0.8 - - - -
48D GLU* 1.3 72.1 - - - +
50D ILE* 1.3 59.7 + - - +
51D GLY* 3.4 31.0 + - - -
52D ARG* 3.8 7.4 - - + -
61D LYS* 4.1 11.2 - - + -
62D TYR 3.9 6.7 - - - -
63D ASP* 3.7 34.0 - - + +
66D PHE* 3.5 12.0 - - - -
111D MET* 3.9 17.9 - - + -
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Residues in contact with ILE 50 (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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38D TRP* 2.8 22.0 + - + +
39D VAL 4.3 0.2 - - - -
40D LYS* 4.0 9.4 - - + +
48D GLU 4.1 5.6 - - - +
49D TRP* 1.3 73.7 - - - +
51D GLY* 1.3 57.5 + - - +
62D TYR* 3.5 5.9 - - + +
63D ASP* 2.9 27.7 + - - +
66D PHE* 3.7 35.3 - - + +
70D ALA* 3.4 31.6 - - + -
72D ILE* 4.3 6.1 - - + -
83D LEU* 3.9 20.9 - - + -
85D LEU* 4.9 2.0 - - + -
96D TYR* 3.6 37.9 - - + -
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Residues in contact with GLY 51 (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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38D TRP 3.0 24.6 + - - -
49D TRP* 3.4 20.5 + - - -
50D ILE* 1.3 81.8 - - - +
52D ARG* 1.3 62.5 + - - +
61D LYS 3.1 14.6 - - - -
62D TYR* 3.9 0.9 - - - -
72D ILE* 3.4 13.4 - - - +
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Residues in contact with ARG 52 (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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100C TYR* 3.2 19.2 + - + -
35D TYR* 3.9 24.5 - - - -
36D MET 3.1 12.8 - - - +
37D GLN* 3.4 31.6 - - - +
49D TRP* 3.9 14.4 - - + -
51D GLY* 1.3 75.6 - - - +
53D ILE* 1.3 60.6 + - - +
54D ASP* 3.7 9.9 - - - +
59D LYS 3.2 25.7 + - - -
60D THR* 3.3 8.4 - - - +
61D LYS* 2.8 48.7 + - + +
72D ILE* 3.7 7.8 - - - +
178G GLU* 2.8 22.0 + - - -
179G GLU* 2.6 31.9 + - - +
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Residues in contact with ILE 53 (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 TYR* 3.4 4.3 - - - -
36D MET* 2.9 49.2 + - + +
52D ARG* 1.3 78.6 - - - +
54D ASP* 1.3 70.7 + - - +
55D PRO* 3.2 13.4 - - + +
58D ASP* 4.1 18.4 - - + +
59D LYS 3.4 5.8 - - - +
60D THR* 3.7 13.2 - - + -
72D ILE* 3.6 29.6 - - + +
73D THR* 3.6 17.9 - - - +
74D ALA* 3.6 31.4 - - + +
81D ALA* 4.7 2.2 - - + -
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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