Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 3T2D
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.6 17.9 + - - +
42A ILE* 3.7 6.2 - - - +
43A ILE* 1.4 75.3 - - - +
45A TYR* 1.3 83.7 + - - +
58A MET* 3.4 2.4 - - - -
59A THR* 3.0 38.2 + - - +
286A ARG* 3.1 31.0 + - - -
312A GLY 3.9 3.1 - - - +
313A TYR* 3.5 15.1 - - + +
314A LEU* 2.8 33.6 + - + +
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Residues in contact with TYR 45 (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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30A ALA* 3.7 21.4 + - + +
33A LEU* 3.7 38.6 - - + -
34A LYS* 3.3 41.7 - - - +
37A GLN* 3.8 25.1 + - - -
42A ILE* 4.0 9.0 - - + -
44A ASP* 1.3 91.7 + - - +
46A PHE* 1.3 65.6 + - - +
47A VAL* 4.3 3.8 - - + -
57A LEU 3.0 13.2 - - - +
58A MET* 4.5 0.7 - - + -
285A ARG 5.0 1.2 + - - -
286A ARG* 3.2 65.7 + - + +
314A LEU* 3.8 6.8 - - - +
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Residues in contact with PHE 46 (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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45A TYR* 1.3 72.8 - - - +
47A VAL* 1.3 71.5 + - - +
48A TYR* 3.8 16.6 - + + -
55A SER 3.8 1.0 - - - +
57A LEU* 2.9 41.9 + - + +
281A VAL* 4.2 9.6 - - + -
282A ASP 4.1 4.7 - - - -
283A PRO* 4.0 6.3 - - + -
286A ARG* 3.6 37.5 - - - -
287A ILE 3.8 14.4 - - - -
288A ALA* 3.9 26.7 - - + -
305A LEU* 4.2 6.3 - - + -
307A PHE* 3.8 26.9 - + + -
314A LEU* 4.7 1.1 - - + -
316A GLY 3.4 21.8 - - - -
317A GLY 3.5 15.0 - - - -
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Residues in contact with VAL 47 (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* 3.8 38.6 - - + +
29A ALA* 4.0 10.8 - - + -
30A ALA* 3.9 24.5 - - + +
33A LEU* 3.8 25.6 - - + -
45A TYR* 4.3 4.3 - - + -
46A PHE* 1.3 79.0 - - - +
48A TYR* 1.3 66.6 + - - +
54A ILE* 4.3 1.8 - - + -
55A SER 3.5 7.2 - - - +
56A LEU* 4.1 8.7 - - + -
286A ARG 2.9 10.8 + - - +
287A ILE* 3.2 7.8 - - + +
288A ALA 3.0 22.3 + - - +
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Residues in contact with TYR 48 (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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7A ILE* 4.1 12.1 - - - +
26A LEU* 4.0 7.6 - - - -
46A PHE* 3.8 23.1 - + - -
47A VAL* 1.3 81.5 - - - +
49A ASN* 1.3 63.2 + - - +
54A ILE* 3.5 2.4 - - - +
55A SER* 2.8 58.2 + - - +
57A LEU* 4.0 15.4 - - + +
128A ALA* 3.4 27.9 - - + +
129A PHE 5.0 1.5 + - - -
130A ALA* 4.2 19.5 - - + -
278A PHE* 4.2 13.5 - + + -
288A ALA* 3.1 29.2 - - + +
305A LEU* 3.7 26.7 - - + -
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Residues in contact with ASN 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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20A HIS* 3.4 20.3 + - - -
21A VAL* 3.6 25.3 - - + +
26A LEU* 3.7 15.3 - - + +
48A TYR* 1.3 76.7 - - - +
50A VAL* 1.3 66.7 + - - +
51A GLY 2.9 23.0 + - - +
53A ASP 3.1 15.3 - - - +
54A ILE* 4.5 0.2 - - - -
55A SER* 5.8 0.2 - - - -
278A PHE* 3.6 4.4 - - - -
288A ALA 3.5 0.4 + - - -
289A ILE* 3.4 15.0 - - - +
290A GLY* 2.9 48.7 + - - +
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Residues in contact with VAL 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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48A TYR* 5.2 0.4 - - + -
49A ASN* 1.3 78.4 - - - +
51A GLY* 1.3 68.7 + - - +
52A ASP 3.2 0.5 + - - -
53A ASP* 3.1 19.6 + - + +
130A ALA* 3.5 38.6 - - + +
131A ALA 4.8 0.7 - - - -
132A ASP* 3.4 19.6 - - + +
278A PHE* 4.2 16.2 - - + -
291A PRO* 4.1 22.7 - - + -
293A MET* 4.2 3.4 - - + -
301A LYS 3.8 25.4 - - - +
303A GLY* 4.1 11.4 - - - +
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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