Contacts of the strand formed by residues 47 - 53 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F TYR* 5.4 0.9 - - + -
50F PRO* 3.7 32.8 - - + -
93F TYR* 3.7 37.8 - - + -
104F PHE* 3.5 49.8 + - + +
105F GLY 4.9 2.4 + - - +
39H VAL* 3.8 19.7 - - + -
40H LYS 3.8 1.3 - - - -
41H GLN* 3.5 35.2 - - + +
45H GLN 5.0 0.6 - - - +
46H GLY* 1.3 71.7 - - - -
48H GLU* 1.3 57.6 + - - +
97H TYR* 4.5 5.2 - - + -
114H TRP* 4.3 3.6 - - + -
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PHE* 4.9 0.2 - - - -
39H VAL* 3.7 3.0 - - - +
40H LYS* 2.7 63.4 + - + +
42H ARG* 4.9 11.9 + - - +
45H GLN* 5.3 6.4 - - - +
46H GLY 4.6 3.0 - - - +
47H LEU* 1.3 74.9 - - - +
49H TRP* 1.3 64.6 + - - +
50H ILE* 4.1 0.3 - - - +
63H ASP* 6.2 0.2 - - - +
65H LYS* 4.8 14.5 - - + +
66H PHE* 3.4 31.8 - - + -
802H NA 4.2 9.0 - - - -
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Residues in contact with TRP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F TYR* 3.5 26.0 - + + -
101F PRO* 3.6 27.8 - - + -
102F LEU* 3.3 39.4 + - + +
104F PHE* 4.2 14.2 - - + -
37H GLN* 2.8 25.4 + - + -
38H TRP 3.9 12.3 - - - -
39H VAL* 4.3 7.6 - - + +
47H LEU 4.2 0.6 - - - -
48H GLU* 1.3 72.9 - - - +
50H ILE* 1.3 59.4 + - - +
51H GLY* 3.4 31.9 + - - -
52H ARG* 3.8 14.6 - - + -
61H LYS* 4.1 10.5 - - + -
62H TYR 3.9 5.8 - - - -
63H ASP* 3.7 34.4 - - + +
66H PHE* 3.5 12.1 - - - -
111H MET* 3.9 18.4 - - + -
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Residues in contact with ILE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H TRP* 2.8 22.9 + - + +
40H LYS* 3.9 9.6 - - + +
48H GLU 4.1 4.9 - - - +
49H TRP* 1.3 74.2 - - - +
51H GLY* 1.3 57.3 + - - +
62H TYR* 3.5 5.7 - - + +
63H ASP* 2.9 26.8 + - - +
66H PHE* 3.7 36.6 - - + +
70H ALA* 3.4 31.9 - - + -
72H ILE* 4.3 6.5 - - + -
83H LEU* 3.9 21.1 - - + -
85H LEU* 4.8 1.8 - - + -
96H TYR* 3.6 37.7 - - + -
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Residues in contact with GLY 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H TRP 3.0 24.4 + - - -
49H TRP* 3.4 21.0 + - - -
50H ILE* 1.3 82.0 - - - +
52H ARG* 1.3 62.2 + - - +
61H LYS 3.1 14.4 - - - -
62H TYR* 3.9 0.7 - - - -
72H ILE* 3.4 14.5 - - - +
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Residues in contact with ARG 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F TYR* 3.3 20.8 + - + -
35H TYR* 3.9 33.0 - - - -
36H MET 3.2 12.6 - - - +
37H GLN* 3.3 26.9 - - - +
49H TRP* 3.8 11.7 - - + -
51H GLY* 1.3 73.9 - - - +
53H ILE* 1.3 60.5 + - - +
54H ASP* 3.7 9.9 - - - +
59H LYS 3.1 26.1 + - - -
60H THR* 3.3 6.9 - - - +
61H LYS* 2.8 49.1 + - + +
72H ILE* 3.7 7.0 - - - +
178I GLU* 3.0 20.2 + - - -
179I GLU* 2.6 33.9 + - - +
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Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H TYR* 3.4 4.5 - - - -
36H MET* 2.9 49.5 + - + +
52H ARG* 1.3 79.1 - - - +
54H ASP* 1.3 71.3 + - - +
55H PRO* 3.2 13.0 - - + +
58H ASP* 4.1 17.5 - - + +
59H LYS 3.4 5.6 - - - +
60H THR* 3.7 20.2 - - + -
72H ILE* 3.6 22.0 - - + +
73H THR* 3.6 17.9 - - - +
74H ALA* 3.6 31.6 - - + +
81H ALA* 4.7 2.5 - - + -
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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