Contacts of the strand formed by residues 47 - 54 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 4.1 18.0 + - - -
43B LEU* 3.7 37.1 + - + -
45B ARG* 3.3 25.1 - - - +
46B ALA* 1.3 75.3 - - - +
48B SER* 1.3 61.4 - - - +
49B LEU* 3.5 27.4 - - + +
64B TYR* 3.7 6.8 - - - -
65B LYS* 2.9 68.5 + - + +
148B GLN* 3.4 6.5 - - - +
149B SER 3.5 23.3 - - - +
150B PHE* 3.5 20.6 - + - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 1.3 74.0 - - - +
49B LEU* 1.3 61.3 + - - +
50B PHE 3.6 6.6 + - - -
51B SER* 3.7 10.2 - - - -
62B LEU* 3.2 22.8 - - - +
63B VAL 3.9 1.1 - - - -
64B TYR* 3.9 9.2 - - - -
134B GLY 5.0 4.0 + - - -
135B GLN 4.0 3.2 + - - -
136B GLU* 3.5 37.9 - - - -
148B GLN 3.0 10.3 + - - +
150B PHE* 3.5 24.6 + - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.6 33.8 - - + -
39B ALA* 4.3 9.2 - - + -
47B TYR* 3.5 22.9 + - + -
48B SER* 1.3 75.0 - - - +
50B PHE* 1.3 60.7 + - - +
63B VAL* 2.8 24.8 + - + +
65B LYS* 3.9 35.9 - - + +
71B TYR* 4.6 1.8 - - + -
94B ILE* 4.1 15.9 - - + -
132B VAL 5.1 0.9 - - - -
133B LEU* 3.6 21.2 - - - +
134B GLY 5.0 0.2 + - - -
150B PHE* 3.7 20.2 - - + -
154B ILE* 4.0 14.5 - - + +
157B LEU* 5.9 0.2 - - - +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.4 1.3 - - + -
35B LEU* 3.4 42.4 - - + -
37B PHE* 4.7 3.8 - - + -
48B SER* 3.6 1.7 + - - -
49B LEU* 1.3 80.9 - - + +
51B SER* 1.3 59.7 + - - +
52B TYR* 4.0 23.3 - + + -
61B LEU* 4.2 19.5 - - + -
62B LEU* 3.4 6.1 - - - +
63B VAL* 3.0 32.0 + - + -
131B ILE* 3.5 28.7 - - + -
132B VAL 4.2 3.1 - - - -
133B LEU* 4.1 7.9 - - + -
157B LEU* 4.0 16.6 - - + -
159B MET* 4.0 23.3 - - - -
183B LEU* 4.0 12.8 - - + -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.7 9.4 + - - -
50B PHE* 1.3 73.5 - - - +
52B TYR* 1.3 60.6 + - - +
53B ASN* 4.3 3.5 + - - -
62B LEU* 4.0 8.6 - - - +
131B ILE* 3.2 5.1 - - - +
132B VAL 2.9 37.1 + - - -
135B GLN 3.6 23.3 - - - -
136B GLU* 4.2 4.7 + - - -
137B GLN* 2.9 39.9 + - - +
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.9 21.1 - - + +
30B LEU* 4.3 3.7 - - + +
50B PHE* 4.0 14.6 - + + -
51B SER* 1.3 74.8 + - - +
53B ASN* 1.3 67.3 + - - +
54B THR* 3.8 8.3 - - + -
59B ASN* 4.3 0.3 - - - -
60B GLU* 3.4 12.3 + - + -
61B LEU* 2.9 69.5 + - + +
62B LEU* 5.2 0.4 - - - +
125B VAL* 3.7 14.8 - - + +
126B GLU 2.7 29.5 + - - -
127B ALA* 4.1 2.1 - - - -
129B PRO* 3.4 37.3 - - + +
130B LYS 3.5 4.5 - - - -
131B ILE* 3.8 17.7 - - + -
159B MET* 4.8 3.8 - - + -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 4.3 4.0 + - - -
52B TYR* 1.3 81.2 + - - +
54B THR* 1.3 65.5 + - - +
57B ARG 3.5 11.6 + - - +
58B ASP* 2.9 28.8 + - - +
59B ASN* 2.9 21.1 + - - +
60B GLU* 4.2 0.7 - - - -
62B LEU* 5.9 0.2 - - - +
129B PRO* 3.4 2.6 - - - +
130B LYS 2.9 31.2 + - - -
136B GLU* 5.0 0.5 - - - +
137B GLN* 3.4 25.5 + - - +
139B SER 3.1 31.6 + - - +
140B TYR* 3.6 6.4 - - - -
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.8 13.2 - - + -
53B ASN* 1.3 79.3 - - - +
55B GLN* 1.3 60.4 + - - +
56B GLY 3.1 1.0 + - - -
57B ARG* 2.9 46.0 + - - +
60B GLU* 3.8 6.4 - - + +
126B GLU* 3.3 43.4 - - + +
127B ALA 3.4 17.9 - - - +
128B GLN 4.4 0.4 - - - -
129B PRO* 4.1 4.5 - - + -
139B SER 5.7 0.2 - - - -
140B TYR* 3.4 17.7 - - - +
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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