Contacts of the strand formed by residues 47 - 54 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ALA* 6.0 0.7 - - - +
41L SER* 4.0 19.7 + - - -
43L LEU* 3.7 39.6 + - + -
45L ARG* 3.4 22.9 - - - +
46L ALA* 1.3 74.4 - - - +
48L SER* 1.3 61.2 + - - +
49L LEU* 3.6 28.2 - - + +
64L TYR* 3.5 8.1 - - - -
65L LYS* 2.9 74.3 + - + +
148L GLN* 3.4 7.2 - - - +
149L SER 3.6 23.3 - - - +
150L PHE* 3.6 19.0 - + - -
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Residues in contact with SER 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L TYR* 1.3 74.5 - - - +
49L LEU* 1.3 60.6 + - - +
50L PHE 3.7 5.5 + - - -
51L SER* 3.7 9.7 + - - -
62L LEU* 3.2 22.7 - - - +
63L VAL 3.9 3.8 - - - -
64L TYR* 3.9 5.2 - - - -
134L GLY 4.9 5.2 + - - -
135L GLN 4.0 2.9 + - - +
136L GLU* 3.5 38.0 - - - +
148L GLN 3.0 10.1 + - - +
150L PHE* 3.5 23.6 + - - +
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Residues in contact with LEU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 3.4 29.7 - - + -
39L ALA* 4.0 14.1 - - + -
47L TYR* 3.6 33.2 + - + +
48L SER* 1.3 74.8 - - - +
50L PHE* 1.3 61.5 + - - +
63L VAL* 2.8 21.9 + - + +
65L LYS* 4.1 17.7 - - + +
71L TYR* 4.4 6.3 - - + -
94L ILE* 3.9 21.5 - - + -
132L VAL 5.2 0.9 - - - -
133L LEU* 3.7 20.0 - - - +
134L GLY 5.0 0.2 + - - -
150L PHE* 3.7 21.1 - - + -
154L ILE* 3.9 15.3 - - + +
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Residues in contact with PHE 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LEU* 4.4 1.3 - - + -
35L LEU* 3.6 44.4 - - + -
37L PHE* 4.6 4.9 - - + -
48L SER* 3.6 2.2 - - - -
49L LEU* 1.3 80.2 - - - +
51L SER* 1.3 60.3 + - - +
52L TYR* 4.0 27.1 - + + -
61L LEU* 4.3 14.1 - - + -
62L LEU* 3.3 7.6 - - - +
63L VAL* 2.9 35.3 + - + -
131L ILE* 3.5 27.4 - - + -
132L VAL 4.1 3.8 - - - -
133L LEU* 3.9 15.9 - - + -
157L LEU* 4.0 10.5 - - + -
159L MET* 3.9 14.4 - - - -
183L LEU* 3.8 21.5 - - + -
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Residues in contact with SER 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L SER* 3.7 8.9 + - - -
50L PHE* 1.3 75.7 - - - +
52L TYR* 1.3 61.5 + - - +
53L ASN* 4.3 2.3 + - - -
62L LEU* 4.0 7.8 - - - +
131L ILE* 3.3 4.2 - - - +
132L VAL* 2.8 39.4 + - - -
135L GLN 3.7 22.7 - - - -
136L GLU* 4.0 5.2 + - - -
137L GLN* 3.0 41.2 + - - +
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Residues in contact with TYR 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LEU* 3.6 22.0 - - + +
30L LEU* 4.1 2.9 - - + +
50L PHE* 4.0 14.4 - + + -
51L SER* 1.3 74.4 + - - +
53L ASN* 1.3 68.5 + - - +
54L THR* 3.9 7.2 - - + -
60L GLU* 3.3 5.7 + - + -
61L LEU* 2.9 71.8 + - + +
62L LEU* 4.8 1.0 - - - +
125L VAL* 3.8 19.3 - - + +
126L GLU 2.7 29.3 + - - -
129L PRO* 3.4 29.4 - - + +
130L LYS 3.6 3.8 - - - -
131L ILE* 3.7 23.8 - - + +
159L MET* 4.7 9.4 - - + -
182L ILE* 5.9 0.7 - - + -
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Residues in contact with ASN 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L SER* 4.3 2.4 + - - -
52L TYR* 1.3 82.9 + - - +
54L THR* 1.3 66.5 + - - +
57L ARG 3.6 6.9 + - - +
58L ASP* 3.0 28.8 + - - +
59L ASN* 2.9 25.2 + - - +
60L GLU* 4.3 1.1 - - - -
129L PRO* 3.4 4.3 - - - +
130L LYS 2.9 31.5 + - - -
136L GLU* 4.9 0.3 - - - +
137L GLN* 3.4 26.8 + - - +
139L SER 3.1 31.8 + - - +
140L TYR* 3.6 4.3 - - - -
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Residues in contact with THR 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L TYR* 3.9 12.8 - - + -
53L ASN* 1.3 80.9 - - - +
55L GLN* 1.3 60.2 + - - +
56L GLY 3.2 0.9 + - - -
57L ARG* 2.8 54.5 + - - +
60L GLU* 4.0 5.9 - - + +
126L GLU* 3.5 28.4 - - + +
127L ALA 3.4 25.6 - - - +
128L GLN 4.3 1.1 - - - -
129L PRO* 4.1 3.6 - - + -
139L SER 5.7 0.3 - - - -
140L TYR* 3.5 16.2 + - - +
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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