Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 6J7Z
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 MET 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN 4.3 0.9 - - - +
42A ARG* 1.3 79.8 - - - +
44A VAL* 1.3 63.3 + - - +
45A TRP* 3.5 21.3 + - + +
67A ILE* 3.4 8.5 - - - +
68A THR* 2.9 40.7 + - - +
69A ASP 4.3 3.6 - - - +
70A SER 3.8 10.3 - - - +
72A LEU* 3.7 32.5 - - + -
138A PRO* 3.8 5.8 - - + +
140A ALA* 4.3 7.2 - - + -
167A ILE* 3.6 30.3 - - + -
207A LEU* 5.0 0.2 - - + -
175B LEU* 4.3 11.9 - - + -
178B ARG* 3.6 30.1 - - - +
179B TRP* 4.9 0.7 - - - +
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Residues in contact with VAL 44 (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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43A MET* 1.3 72.9 - - - +
45A TRP* 1.3 58.9 + - - +
46A VAL* 4.1 8.7 - - + -
65A CYS* 3.7 27.8 - - - -
66A LEU 3.7 2.5 - - - -
67A ILE* 3.8 14.4 - - + -
128A VAL* 3.8 15.0 - - + -
132A THR* 3.8 19.1 - - + -
137A CYS* 4.3 8.1 - - + -
138A PRO 3.0 14.6 + - - +
139A LEU* 3.3 18.3 - - + +
140A ALA 2.9 22.7 + - - -
158A PHE* 4.3 4.7 - - + -
162A LEU* 4.3 16.8 - - + -
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Residues in contact with TRP 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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43A MET* 3.5 24.1 - - + +
44A VAL* 1.3 71.8 - - - +
46A VAL* 1.3 61.5 + - - +
65A CYS* 3.2 4.7 - - - -
66A LEU* 2.9 41.1 + - + +
68A THR* 2.7 41.3 + - + +
72A LEU* 3.9 21.8 - - + -
140A ALA* 3.3 16.4 - - + -
141A GLY* 3.8 19.1 - - - -
167A ILE* 5.4 0.2 - - + -
169A VAL* 3.8 23.6 - - + -
200A ILE* 3.7 23.1 - - + +
203A SER* 3.7 27.4 - - - -
204A ILE* 3.7 31.0 - - + -
207A LEU* 3.8 11.0 - - + -
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Residues in contact with VAL 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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44A VAL* 4.1 3.6 - - + -
45A TRP* 1.3 80.0 - - - +
47A ASP* 1.3 66.1 + - - +
48A LEU* 4.8 6.3 - - + -
63A MET* 4.7 4.9 - - + -
64A ALA 3.3 7.4 - - - +
65A CYS* 3.9 21.1 - - + -
139A LEU* 3.5 43.1 - - + -
140A ALA 3.0 14.4 + - - +
141A GLY* 4.4 8.0 - - - -
144A VAL* 4.2 10.4 - - + +
147A ASP* 4.1 10.2 - - + +
151A LEU* 4.3 9.9 - - + -
158A PHE* 4.3 12.6 - - + -
200A ILE* 3.8 5.6 - - - +
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Residues in contact with ASP 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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46A VAL* 1.3 77.2 - - - +
48A LEU* 1.3 65.5 + - - +
49A GLU* 2.8 31.1 - - - +
63A MET* 3.4 2.3 - - - -
64A ALA 2.9 32.1 + - - -
142A ASN 5.4 4.3 + - - +
147A ASP* 3.8 10.3 - - - +
196A ALA* 3.2 40.3 - - + +
199A ALA* 3.4 17.2 - - + +
200A ILE* 3.5 8.7 - - + -
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Residues in contact with LEU 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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46A VAL* 4.8 2.0 - - + -
47A ASP* 1.3 89.2 - - - +
49A GLU* 1.3 74.0 + - - +
50A MET* 4.9 11.6 - - + +
61A ILE* 4.3 12.1 - - + -
62A GLU 3.2 4.3 - - - +
63A MET* 3.6 37.7 - - + -
147A ASP* 3.6 28.8 + - + +
150A PHE* 3.4 43.1 - - + -
151A LEU* 4.2 17.7 - - + -
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Residues in contact with GLU 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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47A ASP* 2.8 32.3 - - - +
48A LEU* 1.3 79.0 - - - +
50A MET* 1.3 67.8 + - - +
61A ILE* 3.5 2.0 - - - +
62A GLU* 2.9 42.5 + - + +
194A HIS* 3.4 33.1 - - + +
196A ALA* 4.1 9.2 - - - -
199A ALA* 4.2 7.8 - - - +
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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