Contacts of the strand formed by residues 47 - 54 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F SER* 4.0 18.5 + - - -
43F LEU* 3.8 37.7 + - + -
45F ARG* 3.2 25.1 - - - +
46F ALA* 1.3 74.9 - - - +
48F SER* 1.3 62.1 + - - +
49F LEU* 3.8 20.7 - - + +
64F TYR* 3.6 7.0 - - - -
65F LYS* 2.8 73.1 + - + +
148F GLN* 3.5 8.3 - - - +
149F SER 3.6 23.6 - - - +
150F PHE* 3.6 26.2 - + - -
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Residues in contact with SER 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F TYR* 1.3 71.6 - - - +
49F LEU* 1.3 62.8 + - - +
50F PHE 3.6 6.6 + - - -
51F SER* 3.7 12.1 - - - -
62F LEU* 3.3 19.2 - - - +
63F VAL 3.8 1.3 - - - -
64F TYR* 3.6 9.8 - - - -
132F VAL 5.1 0.2 + - - -
134F GLY 4.9 4.5 + - - -
135F GLN 3.8 4.6 + - - +
136F GLU* 3.4 37.7 - - - -
148F GLN 3.1 9.6 + - - +
150F PHE* 3.6 23.2 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 3.8 22.3 - - + -
39F ALA* 3.9 19.7 - - + -
47F TYR* 3.7 26.4 + - + +
48F SER* 1.3 74.1 - - - +
50F PHE* 1.3 62.0 + - - +
63F VAL* 2.8 22.1 + - + +
65F LYS* 4.3 21.1 - - + +
71F TYR* 4.5 7.2 - - + -
94F ILE* 3.8 25.6 - - + -
132F VAL 5.1 1.1 - - - -
133F LEU* 3.7 19.3 - - - +
134F GLY 5.0 0.5 + - - -
150F PHE* 3.8 19.7 - - + -
154F ILE* 4.1 15.3 - - + +
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Residues in contact with PHE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 4.1 2.2 - - + -
35F LEU* 3.4 42.2 - - + -
37F PHE* 4.6 4.5 - + + -
48F SER* 3.6 2.4 + - - -
49F LEU* 1.3 80.6 - - - +
51F SER* 1.3 59.8 + - - +
52F TYR* 4.0 24.0 - + + -
61F LEU* 4.4 13.0 - - + -
62F LEU* 3.3 7.8 - - - +
63F VAL* 2.9 34.1 + - + -
131F ILE* 3.4 30.7 - - + -
132F VAL 4.1 3.1 - - - -
133F LEU* 3.9 15.3 - - + -
157F LEU* 3.9 13.5 - - + -
159F MET* 4.0 23.1 - - - -
183F LEU* 4.0 12.8 - - + -
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Residues in contact with SER 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F SER* 3.7 7.9 - - - -
50F PHE* 1.3 74.5 - - - +
52F TYR* 1.3 60.7 + - - +
53F ASN* 4.2 2.8 + - - -
62F LEU* 4.1 7.5 - - - +
131F ILE* 3.2 2.8 - - - +
132F VAL 2.8 38.7 + - - +
135F GLN 3.7 23.3 - - - -
136F GLU* 4.0 5.9 + - - -
137F GLN* 2.9 41.8 + - - +
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Residues in contact with TYR 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 3.5 22.7 - - + +
30F LEU* 3.8 12.8 - - + +
50F PHE* 4.0 11.9 - + + -
51F SER* 1.3 73.2 + - - +
53F ASN* 1.3 65.6 + - - +
54F THR* 3.9 6.7 - - + -
59F ASN* 4.3 0.3 - - - -
60F GLU* 3.3 8.1 + - + -
61F LEU* 3.0 64.7 + - + +
62F LEU* 5.2 0.6 - - - +
125F VAL* 3.7 20.1 - - + +
126F GLU 2.7 29.8 + - - -
127F ALA* 3.9 0.2 - - - -
129F PRO* 3.4 28.7 - - + +
130F LYS 3.5 4.7 - - - -
131F ILE* 3.7 23.3 - - + +
159F MET* 4.5 4.5 - - + -
182F ILE* 6.1 0.2 - - + -
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Residues in contact with ASN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F SER* 4.2 3.8 + - - -
52F TYR* 1.3 77.8 + - - +
54F THR* 1.3 65.8 + - - +
57F ARG 3.5 10.6 + - - +
58F ASP* 3.1 27.2 + - - +
59F ASN* 3.0 20.6 + - - +
60F GLU* 4.3 0.7 - - - -
129F PRO* 3.3 3.3 - - - +
130F LYS 2.8 32.4 + - - -
136F GLU* 4.9 0.2 - - - +
137F GLN* 3.5 32.3 + - - +
138F ASP 3.9 0.4 - - - -
139F SER* 2.9 30.0 + - - +
140F TYR* 3.6 3.8 - - - -
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TYR* 3.9 12.3 - - + -
53F ASN* 1.3 81.4 - - - +
55F GLN* 1.3 54.9 + - - +
56F GLY 3.1 1.0 + - - -
57F ARG* 2.8 52.4 + - - +
60F GLU* 3.9 6.7 - - + +
126F GLU* 3.4 44.1 - - + +
127F ALA 3.6 17.7 - - - +
128F GLN 4.5 0.7 - - - -
129F PRO* 4.1 4.0 - - + -
140F TYR* 3.4 13.4 + - - +
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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