Contacts of the strand formed by residues 47 - 51 (chain A) in PDB entry 3EHW
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 GLY 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.8 21.7 - - - +
41A GLY 4.6 0.3 + - - -
45A ALA* 3.1 8.2 - - - +
46A ALA* 1.3 80.7 - - - +
48A TYR* 1.3 64.2 + - - -
49A ASP* 3.9 5.0 + - - +
131A GLN* 3.8 24.2 + - - +
132A LEU 3.2 14.8 - - - -
133A ILE* 4.0 3.6 - - - +
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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
----------------------------------------------------------
26A LEU* 3.8 22.2 - - + -
38A PRO* 3.8 17.7 - - + -
39A THR* 3.6 23.1 - - - -
40A ARG* 3.5 43.2 + - + -
47A GLY* 1.3 71.6 - - - -
49A ASP* 1.3 64.0 + - - +
50A LEU* 3.5 1.2 + - - +
131A GLN* 4.1 0.2 - - - -
132A LEU* 2.7 47.2 + - + +
134A CYS* 5.9 1.1 - - - -
140B PRO* 2.9 34.4 + - + -
141B GLU* 3.8 2.6 + - - -
142B ILE* 3.2 44.0 + - + +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 3.3 26.3 - - - +
39A THR* 2.7 22.4 + - - +
41A GLY* 4.1 14.4 + - - -
47A GLY 4.3 4.5 - - - +
48A TYR* 1.3 72.2 - - - +
50A LEU* 1.3 59.9 + - - +
51A TYR* 3.7 4.0 - - - -
85A ARG* 4.3 10.7 + - - -
128A ARG* 3.1 49.8 + - + -
130A ALA 3.5 6.6 - - - +
131A GLN* 3.7 15.8 - - - +
165A MG 4.1 10.3 - - - -
161C THR* 4.4 1.6 + - - -
777C DUP 5.0 1.0 + - - -
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Residues in contact with LEU 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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38A PRO* 4.1 23.8 - - + -
48A TYR 3.9 7.9 - - - +
49A ASP* 1.3 72.6 - - - +
51A TYR* 1.3 62.1 + - - +
68A THR* 4.2 17.3 - - + -
70A ILE* 4.4 12.1 - - + -
72A ILE* 6.1 0.2 - - + -
82A VAL* 4.1 20.9 - - + -
109A VAL* 4.6 8.7 - - + -
111A VAL* 3.8 26.5 - - + -
128A ARG* 3.3 2.8 - - - -
129A ILE* 3.0 29.4 + - - +
130A ALA* 2.8 16.1 + - + +
131A GLN 4.3 3.6 - - - -
132A LEU* 4.0 32.5 - - + +
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Residues in contact with TYR 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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36A THR* 3.5 52.2 + - + +
37A ALA 3.4 19.7 - - - -
38A PRO* 4.3 0.2 - - + -
39A THR* 2.7 33.8 + - - +
49A ASP 3.7 14.6 - - - -
50A LEU* 1.3 74.7 - - - +
52A SER* 1.3 67.0 + - - +
53A ALA* 3.5 2.4 + - - -
68A THR* 3.7 22.7 - - - +
126A GLY* 3.1 26.5 - - - -
127A ASP 3.2 4.9 - - - +
128A ARG* 3.4 28.3 + - + -
129A ILE* 4.8 2.0 - - - -
164C ASN* 4.2 13.1 + - - -
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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