Contacts of the strand formed by residues 47 - 54 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 6.1 0.5 - - - +
41A SER* 4.0 17.7 + - - -
43A LEU* 3.8 37.4 + - + -
45A ARG* 3.3 25.4 - - - +
46A ALA* 1.3 73.8 - - - +
48A SER* 1.3 63.2 + - - +
49A LEU* 3.7 22.1 - - + +
64A TYR* 3.5 8.1 - - - -
65A LYS* 2.8 71.5 + - + +
148A GLN* 3.5 7.6 - - - +
149A SER 3.5 23.6 - - - +
150A PHE* 3.5 26.2 - + - -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 1.3 72.9 - - - +
49A LEU* 1.3 62.7 + - - +
50A PHE 3.6 3.8 + - - -
51A SER* 3.6 14.4 + - - -
62A LEU* 3.3 19.6 - - - +
63A VAL 3.8 1.6 - - - -
64A TYR* 3.8 8.3 - - - -
132A VAL 5.1 0.2 + - - -
134A GLY 4.9 4.3 + - - -
135A GLN 3.8 3.8 + - - -
136A GLU* 3.6 37.9 - - - -
148A GLN 3.1 10.1 + - - +
150A PHE* 3.5 23.9 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.8 22.4 - - + -
39A ALA* 3.9 20.0 - - + -
47A TYR* 3.7 26.2 + - + +
48A SER* 1.3 74.9 - - - +
50A PHE* 1.3 61.4 + - - +
63A VAL* 2.8 23.9 + - + +
65A LYS* 4.2 20.9 - - + +
71A TYR* 4.5 6.7 - - + -
94A ILE* 3.8 24.5 - - + -
132A VAL 5.1 0.7 - - - -
133A LEU* 3.8 20.3 - - - +
134A GLY 5.0 0.6 + - - -
150A PHE* 3.9 17.0 - - + -
154A ILE* 4.0 17.9 - - + +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.3 4.3 - - + -
35A LEU* 3.5 42.2 - - + -
37A PHE* 4.7 4.7 - - + -
48A SER* 3.6 2.0 + - - -
49A LEU* 1.3 79.6 - - - +
51A SER* 1.3 57.8 + - - +
52A TYR* 3.9 24.7 - + + -
61A LEU* 4.3 19.1 - - + -
62A LEU* 3.3 7.3 - - - +
63A VAL* 2.9 36.9 + - + -
131A ILE* 3.5 27.8 - - + -
132A VAL 4.1 3.1 - - - -
133A LEU* 3.9 15.5 - - + -
157A LEU* 4.1 6.1 - - + -
159A MET* 3.9 23.1 - - - -
183A LEU* 3.8 13.0 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 3.6 8.5 - - - -
50A PHE* 1.3 73.7 - - - +
52A TYR* 1.3 60.8 + - - +
53A ASN* 4.4 2.6 + - - -
62A LEU* 3.9 8.6 - - - +
131A ILE* 3.3 3.3 - - - +
132A VAL 2.8 38.5 + - - -
135A GLN 3.6 23.3 - - - -
136A GLU* 4.1 4.5 + - - -
137A GLN* 3.1 41.0 + - - +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.0 16.1 - - + +
30A LEU* 4.2 9.9 - - + +
50A PHE* 3.9 13.2 - + + -
51A SER* 1.3 73.7 + - - +
53A ASN* 1.3 67.7 + - - +
54A THR* 3.9 7.4 - - + -
59A ASN* 4.2 0.3 - - - -
60A GLU* 3.3 7.0 + - + -
61A LEU* 2.9 75.6 + - + +
62A LEU* 5.1 0.6 - - - +
125A VAL* 3.7 20.1 - - + +
126A GLU 2.6 29.8 + - - -
127A ALA* 4.0 0.3 - - - -
129A PRO* 3.4 31.8 - - + +
130A LYS 3.5 4.3 - - - -
131A ILE* 3.7 22.2 - - + +
159A MET* 4.7 4.5 - - + -
182A ILE* 6.1 0.9 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 4.4 3.1 + - - -
52A TYR* 1.3 78.8 + - - +
54A THR* 1.3 64.7 + - - +
57A ARG 3.6 10.5 + - - +
58A ASP* 2.9 27.0 + - - +
59A ASN* 3.0 21.5 + - - +
60A GLU* 4.3 0.4 - - - -
62A LEU* 6.0 0.2 - - - +
129A PRO* 3.2 4.6 - - - +
130A LYS 2.8 31.7 + - - -
136A GLU* 4.9 0.3 - - - +
137A GLN* 3.4 28.7 + - - +
139A SER 2.8 33.5 + - - +
140A TYR* 3.7 3.9 - - - -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.9 12.3 - - + -
53A ASN* 1.3 78.5 - - - +
55A GLN* 1.3 59.5 + - - +
56A GLY 3.1 0.9 + - - -
57A ARG* 2.9 46.3 + - - +
60A GLU* 3.9 6.8 - - + +
126A GLU* 3.6 37.1 + - + +
127A ALA 3.4 25.6 - - - +
128A GLN 4.2 1.3 - - - -
129A PRO* 4.0 4.3 - - + -
139A SER 5.6 0.3 - - - -
140A TYR* 3.3 17.3 + - - +
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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