Contacts of the strand formed by residues 47 - 54 (chain H) in PDB entry 2A3W
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 47 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H SER* 4.0 18.5 + - - -
43H LEU* 3.8 36.4 + - + -
45H ARG* 3.3 24.5 - - - +
46H ALA* 1.3 74.9 - - - +
48H SER* 1.3 62.8 + - - +
49H LEU* 3.5 33.7 - - + -
64H TYR* 3.7 7.9 - - - -
65H LYS* 2.9 66.1 + - + +
148H GLN* 3.7 7.6 - - - +
149H SER 3.6 22.0 - - - +
150H PHE* 3.5 22.4 - + - -
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Residues in contact with SER 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H TYR* 1.3 74.9 - - - +
49H LEU* 1.3 61.3 + - - +
50H PHE 3.6 6.8 + - - -
51H SER* 3.7 11.8 + - - -
62H LEU* 3.3 19.8 - - - +
63H VAL 3.8 4.0 - - - -
64H TYR* 3.9 6.2 - - - -
134H GLY 5.0 3.8 + - - -
135H GLN 4.0 3.1 + - - +
136H GLU* 3.5 37.7 - - - -
148H GLN 3.2 9.3 + - - +
150H PHE* 3.5 24.3 + - - +
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.5 29.4 - - + -
39H ALA* 4.2 12.6 - - + -
47H TYR* 3.5 35.7 + - + -
48H SER* 1.3 74.5 - - - +
50H PHE* 1.3 61.4 + - - +
63H VAL* 2.8 22.6 + - + +
65H LYS* 4.0 18.8 - - + +
71H TYR* 4.6 5.6 - - + -
94H ILE* 4.1 17.7 - - + -
132H VAL 5.1 1.1 - - - -
133H LEU* 3.7 20.3 - - - +
134H GLY 5.1 0.4 + - - -
150H PHE* 3.6 22.2 - - + -
154H ILE* 4.1 15.4 - - + +
157H LEU* 5.8 0.5 - - - +
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Residues in contact with PHE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 4.2 2.7 - - + -
35H LEU* 3.5 48.2 - - + -
37H PHE* 4.7 3.4 - - + -
48H SER* 3.6 2.0 + - - -
49H LEU* 1.3 80.7 - - + +
51H SER* 1.3 60.1 + - - +
52H TYR* 3.9 28.5 - + + -
61H LEU* 4.3 13.9 - - + -
62H LEU* 3.3 7.4 - - - +
63H VAL* 2.9 32.4 + - + -
131H ILE* 3.5 29.2 - - + -
132H VAL 4.1 3.1 - - - -
133H LEU* 3.9 14.8 - - + -
157H LEU* 4.0 12.1 - - + -
159H MET* 4.0 9.2 - - - -
183H LEU* 3.9 20.2 - - + -
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Residues in contact with SER 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H SER* 3.7 8.9 + - - -
50H PHE* 1.3 74.6 - - - +
52H TYR* 1.3 59.7 + - - +
53H ASN* 4.4 2.8 + - - -
62H LEU* 4.0 8.7 - - - +
131H ILE* 3.3 3.5 - - - +
132H VAL 2.8 38.0 + - - -
135H GLN 3.7 23.1 - - - -
136H GLU* 4.1 4.3 + - - -
137H GLN* 3.0 41.3 + - - +
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Residues in contact with TYR 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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26H LEU* 4.1 11.6 - - + +
30H LEU* 4.0 14.1 - - + +
50H PHE* 3.9 13.5 - + + -
51H SER* 1.3 75.0 + - - +
53H ASN* 1.3 67.8 + - - +
54H THR* 3.9 7.4 - - + -
60H GLU* 3.4 5.4 + - + +
61H LEU* 2.9 70.6 + - + +
62H LEU* 5.2 0.2 - - - +
125H VAL* 3.7 21.6 - - + +
126H GLU 2.8 28.4 + - - -
129H PRO* 3.4 33.7 - - + +
130H LYS 3.5 4.7 - - - -
131H ILE* 3.8 23.3 - - + +
159H MET* 4.7 4.0 - - + -
182H ILE* 6.0 0.9 - - + -
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Residues in contact with ASN 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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51H SER* 4.4 3.8 + - - -
52H TYR* 1.3 80.5 + - - +
54H THR* 1.3 66.5 + - - +
57H ARG 3.6 10.2 + - - +
58H ASP* 2.9 28.7 + - - +
59H ASN* 2.8 23.7 + - - +
60H GLU* 4.4 0.4 - - - -
129H PRO* 3.3 3.6 - - - +
130H LYS 2.8 33.6 + - - -
137H GLN* 3.4 26.2 + - - +
138H ASP 4.0 0.2 - - - -
139H SER* 3.2 32.2 + - - +
140H TYR* 3.6 3.5 - - - -
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Residues in contact with THR 54 (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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52H TYR* 3.9 14.4 - - + -
53H ASN* 1.3 80.6 - - - +
55H GLN* 1.3 68.7 + - - +
56H GLY 3.1 0.9 + - - -
57H ARG* 2.8 41.0 + - - +
60H GLU* 3.9 6.1 - - + +
126H GLU* 3.5 33.5 - - + +
127H ALA 3.5 24.9 - - - +
128H GLN 4.3 0.9 - - - -
129H PRO* 4.0 4.3 - - + -
139H SER 5.8 0.2 - - - -
140H TYR* 3.5 14.8 + - - +
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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