Contacts of the strand formed by residues 47 - 53 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42J TYR* 5.4 1.1 - - + -
50J PRO* 3.7 34.3 - - + -
93J TYR* 3.8 29.5 - - + -
104J PHE* 3.6 54.0 + - + +
105J GLY 5.0 1.1 + - - +
39K VAL* 3.8 21.5 - - + -
40K LYS 3.8 1.6 - - - -
41K GLN* 3.5 34.8 - - + +
46K GLY* 1.3 72.2 - - - -
48K GLU* 1.3 59.8 + - - +
97K TYR* 4.5 5.6 - - + -
114K TRP* 4.3 4.0 - - + -
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Residues in contact with GLU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K VAL* 3.5 3.4 - - - +
40K LYS* 2.7 63.2 + - + +
42K ARG* 4.8 8.3 - - - +
46K GLY 4.6 2.3 - - - +
47K LEU* 1.3 74.4 - - - +
49K TRP* 1.3 65.5 + - - +
50K ILE* 3.5 1.2 + - - +
63K ASP* 6.1 0.2 - - - +
65K LYS* 4.8 16.7 + - + +
66K PHE* 3.4 32.6 - - + -
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Residues in contact with TRP 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J TYR* 3.4 35.0 - + + -
101J PRO* 3.6 26.9 - - + -
102J LEU* 3.4 37.3 + - + +
104J PHE* 4.4 11.0 - - + -
37K GLN* 2.8 26.0 + - + -
38K TRP 3.9 12.8 - - - -
39K VAL* 4.4 8.2 - - + +
47K LEU 4.3 0.6 - - - -
48K GLU* 1.3 72.1 - - - +
50K ILE* 1.4 59.5 + - - +
51K GLY* 3.4 31.4 + - - -
52K ARG* 3.8 7.4 - - + -
61K LYS* 4.1 11.2 - - + -
62K TYR 3.9 6.3 - - - -
63K ASP* 3.7 35.7 - - + +
66K PHE* 3.5 11.4 - - - -
111K MET* 3.9 17.0 - - + -
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Residues in contact with ILE 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K TRP* 2.8 23.5 + - + +
40K LYS* 3.9 14.4 - - + +
48K GLU 4.1 0.2 - - - +
49K TRP* 1.4 73.7 - - - +
51K GLY* 1.3 58.8 + - - +
62K TYR* 3.5 5.6 - - + +
63K ASP* 2.9 27.0 + - - +
66K PHE* 3.7 36.0 - - + +
70K ALA* 3.4 30.5 - - + -
72K ILE* 4.3 6.5 - - + -
83K LEU* 3.9 20.9 - - + -
85K LEU* 4.9 1.8 - - + -
96K TYR* 3.6 37.9 - - + -
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Residues in contact with GLY 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K TRP 3.0 23.7 + - - -
49K TRP* 3.4 20.5 + - - -
50K ILE* 1.3 82.2 - - - +
52K ARG* 1.3 61.9 + - - +
61K LYS 3.1 14.8 - - - -
62K TYR* 3.9 0.9 - - - -
72K ILE* 3.4 13.7 - - - +
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Residues in contact with ARG 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J TYR* 3.2 20.8 + - + -
35K TYR* 3.9 23.7 - - - -
36K MET 3.2 12.6 - - - +
37K GLN* 3.4 30.1 - - - +
49K TRP* 3.8 14.8 - - + -
51K GLY* 1.3 75.5 - - - +
53K ILE* 1.3 60.3 + - - +
54K ASP* 3.7 9.7 - - - +
59K LYS 3.1 26.3 + - - -
60K THR* 3.3 6.2 - - - -
61K LYS* 2.8 49.8 + - + +
72K ILE* 3.7 7.6 - - - +
178L GLU* 2.9 21.4 + - - -
179L GLU* 2.6 32.1 + - - +
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Residues in contact with ILE 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K TYR* 3.4 4.2 - - - -
36K MET* 2.9 50.0 + - + +
52K ARG* 1.3 78.6 - - - +
54K ASP* 1.3 70.6 + - - +
55K PRO* 3.2 13.6 - - + +
58K ASP* 4.1 18.2 - - + +
59K LYS 3.4 6.5 - - - +
60K THR* 3.7 20.9 - - + -
72K ILE* 3.6 21.5 - - + +
73K THR* 3.6 17.3 - - - +
74K ALA* 3.6 31.2 - - + +
81K ALA* 4.7 2.7 - - + -
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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