Contacts of the strand formed by residues 105 - 110 (chain D) in PDB entry 4MJI
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 THR 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D PRO* 3.2 23.0 + - + +
9D GLN 3.3 19.7 - - - +
11D LEU* 4.0 16.2 - - + -
21D MET* 3.7 34.6 - - + +
22D ASN 4.4 5.9 + - - -
85D ALA 4.0 0.3 - - - +
86D SER* 3.2 7.9 - - - -
87D TYR* 2.8 38.6 + - - +
88D PHE* 5.0 1.0 - - - -
104D GLY* 1.3 77.6 - - - -
106D GLN* 1.3 63.0 + - - +
107D LEU 3.2 4.3 + - - -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN 4.1 4.2 + - - -
10D ALA* 3.1 21.3 - - + +
11D LEU 2.7 33.9 + - - +
85D ALA 5.7 0.4 - - - -
86D SER* 3.6 21.0 + - - +
105D THR* 1.3 70.9 - - - +
107D LEU* 1.3 59.8 + - - +
108D THR* 4.1 9.8 + - + +
43E GLY* 5.9 2.9 - - - -
177E GLN* 5.5 4.9 + - - -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.3 25.4 - - + +
13D ILE* 4.3 11.9 - - + -
19D ALA* 4.0 30.3 - - + -
21D MET* 4.3 14.4 - - + -
76D ILE* 5.1 3.8 - - + -
79D SER* 5.8 0.4 - - - -
83D ASP* 3.6 14.1 - - + +
84D THR* 3.7 2.6 - - - -
85D ALA 3.1 36.1 + - - +
87D TYR* 3.6 30.7 - - + +
105D THR* 3.2 2.0 + - + -
106D GLN* 1.3 75.2 - - - +
108D THR* 1.3 71.2 + - - +
109D VAL* 4.2 13.5 - - + -
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 5.1 3.5 - - - +
11D LEU 2.7 15.5 + - - -
12D SER* 3.1 18.5 + - - -
13D ILE 3.0 23.7 + - - -
84D THR* 3.5 10.1 - - + -
106D GLN* 4.1 12.2 + - + +
107D LEU* 1.3 77.4 - - - +
109D VAL* 1.3 63.7 + - - +
110D LEU* 3.6 11.2 + - + +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.6 10.8 - - + +
15D GLU* 3.5 40.0 - - + +
79D SER* 3.7 24.0 - - - +
80D ARG 3.3 30.3 - - - +
81D ALA* 4.5 7.4 - - - +
83D ASP* 4.3 6.5 - - + -
84D THR* 2.8 24.2 - - + +
107D LEU* 4.2 17.0 - - + -
108D THR* 1.3 72.7 - - - +
110D LEU* 1.3 58.4 + - - +
111D PRO* 4.8 0.3 - - - +
160D VAL* 5.7 3.5 - - - +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 3.6 32.1 - - - +
13D ILE 3.0 18.3 + - - +
14D GLN* 3.7 8.8 - - - +
15D GLU* 2.9 26.6 + - - +
108D THR* 4.1 11.2 - - + +
109D VAL* 1.3 75.3 - - - +
111D PRO* 1.3 72.3 - - + +
141D SER* 3.4 22.4 - - - +
158D LYS* 3.7 33.0 - - + +
160D VAL* 6.1 1.8 - - + -
171D ASN* 5.7 1.6 - - - +
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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