Contacts of the strand formed by residues 111 - 116 (chain E) 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 SER 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E GLN* 4.5 2.8 - - - +
10E THR 3.5 16.3 + - - -
11E PRO 2.6 28.7 + - - -
12E SER 3.1 4.7 - - - -
13E ASN 4.9 0.7 - - - -
14E LYS 5.8 0.2 - - - -
24E LEU* 4.4 24.6 - - - +
25E ARG 5.0 0.4 + - - -
37E TRP* 6.3 0.2 - - - -
91E ALA 3.7 1.0 - - - +
92E VAL* 3.4 6.1 - - - +
93E TYR* 3.1 34.6 + - - +
110E GLY* 1.3 75.2 + - - -
112E ARG* 1.4 62.8 + - - +
113E LEU* 3.5 3.3 + - - +
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E SER 2.7 13.5 + - - +
13E ASN* 3.2 9.9 - - - +
14E LYS 2.9 25.2 + - - +
41E SER* 5.0 1.4 - - - +
42E LEU* 4.8 15.4 - - - +
90E SER* 4.1 17.8 + - - -
91E ALA* 4.1 19.2 - - - +
92E VAL* 3.8 27.3 - - + +
111E SER* 1.4 68.7 - - - +
113E LEU* 1.3 71.6 + - - +
114E THR* 3.4 25.2 + - - +
155E ASP* 5.8 4.3 + - - -
156E HIS* 3.0 30.8 + - + +
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Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LYS* 3.1 21.5 - - + +
16E THR* 5.1 1.8 - - - +
22E VAL* 3.7 41.5 - - + -
24E LEU* 5.2 6.7 - - + -
82E ILE* 4.3 11.9 - - + -
85E THR* 5.9 0.2 - - - +
89E ASP* 3.3 28.3 - - + +
90E SER* 3.3 2.9 - - - -
91E ALA 3.0 35.8 + - - +
93E TYR* 3.7 17.0 - - + -
111E SER 4.5 4.5 - - - +
112E ARG* 1.3 77.2 + - - +
114E THR* 1.3 61.0 + - - +
115E VAL* 4.2 19.1 - - + -
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Residues in contact with THR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LYS 3.0 7.8 + - - +
15E VAL* 3.6 10.4 - - - +
16E THR 3.4 23.7 + - - +
87E ARG* 6.1 0.9 - - - +
90E SER* 3.5 7.9 - - - +
112E ARG* 3.4 18.4 + - - +
113E LEU* 1.3 72.7 - - - +
115E VAL* 1.3 65.1 + - - +
116E LEU* 3.2 29.1 - - + +
154E PRO* 4.3 11.4 - - + -
155E ASP* 5.5 0.7 + - - -
156E HIS* 2.5 34.4 + - - -
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Residues in contact with VAL 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E THR* 3.4 6.1 - - - +
17E GLU 3.9 10.3 - - - -
18E LYS* 3.9 2.7 - - - +
22E VAL* 5.4 0.7 - - + -
85E THR* 3.2 37.7 - - + +
86E GLU* 3.1 36.1 - - - +
87E ARG* 3.1 22.8 + - - +
89E ASP* 5.0 2.0 - - + -
90E SER* 2.6 17.8 + - - +
113E LEU* 4.2 28.3 - - + -
114E THR* 1.3 78.6 - - - +
116E LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 4.3 13.9 - - + -
16E THR 3.1 16.9 + - - +
17E GLU* 3.4 2.3 - - - -
18E LYS* 3.1 26.2 + - - +
87E ARG* 4.0 15.7 - - - +
114E THR* 3.2 35.0 - - + +
115E VAL* 1.3 75.0 - - - +
117E GLU* 1.3 61.9 - - - +
118E ASP 3.4 20.6 - - - +
119E LEU* 5.1 3.4 - - + -
122E VAL* 3.9 24.9 - - + -
153E TYR* 4.4 24.0 - - + +
154E PRO* 4.3 10.8 - - + -
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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