Contacts of the strand formed by residues 106 - 110 (chain B) in PDB entry 4M83
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 LEU 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS 3.5 3.3 + - - +
9B ILE* 3.6 14.9 - - + -
10B ALA 3.0 24.3 + - - -
104B PRO* 3.3 5.7 - - - +
105B ASP* 1.3 82.0 - - - +
107B VAL* 1.3 82.2 + - - +
108B LEU* 4.2 4.3 - - + +
125B VAL* 4.6 1.3 - - - -
126B PRO* 3.6 19.3 - - + +
128B VAL* 4.4 9.2 - - + -
393B ILE* 4.0 24.2 - - + +
396B GLU* 3.3 47.8 - - + +
397B LEU* 3.9 17.7 - - + +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 3.4 2.5 - - - +
12B PHE* 3.5 29.6 - - + -
104B PRO* 4.1 19.3 - - + -
106B LEU* 1.3 84.3 - - - +
108B LEU* 1.3 64.4 - - - +
109B HIS* 4.6 4.0 - - + -
116B ALA* 4.0 22.0 - - + +
120B ALA* 4.2 22.2 - - + +
123B TRP* 4.2 16.6 - - + -
125B VAL* 4.4 4.5 - - + -
126B PRO 3.0 11.8 + - - +
127B ALA* 3.3 2.5 - - - +
128B VAL 2.8 25.6 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.3 15.5 - - + -
10B ALA 2.8 10.0 + - - +
11B MET* 3.0 16.9 - - + -
12B PHE* 2.7 25.8 + - - -
26B VAL* 5.1 0.2 - - + -
27B ILE* 3.7 29.8 - - + -
30B LEU* 4.0 9.0 - - + -
106B LEU* 4.2 1.3 - - + +
107B VAL* 1.3 74.8 - - - +
109B HIS* 1.3 62.1 + - - +
128B VAL* 3.4 26.2 - - + +
130B LEU* 3.6 24.7 - - + -
393B ILE* 3.7 34.5 - - + -
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 3.9 4.7 - - - -
12B PHE* 3.3 12.6 - - + +
107B VAL* 4.6 5.8 - - + -
108B LEU* 1.3 80.3 - - - +
110B ASP* 1.3 77.2 + - - +
113B SER* 3.9 2.5 + - - -
116B ALA* 3.4 30.7 - - + -
117B ARG* 3.6 45.0 + - + +
127B ALA* 4.7 10.6 - - + +
128B VAL 3.1 15.9 + - - -
129B SER* 3.4 29.7 + - - -
130B LEU* 2.8 32.9 + - - -
185B PRO* 5.8 1.9 - - + +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B MET* 4.1 7.3 - - + +
12B PHE 3.1 7.2 + - - +
13B SER* 3.4 21.8 - - - +
19B HIS* 2.8 46.9 + - - +
22B PRO* 6.0 0.5 - - - +
23B SER* 5.9 0.7 - - - +
109B HIS* 1.3 91.6 + - - +
111B ILE* 1.3 66.0 + - - +
112B THR* 2.7 30.1 + - - +
113B SER* 3.2 9.0 + - - -
130B LEU* 3.4 9.4 - - + +
132B PRO* 3.4 19.4 - - - +
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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