Contacts of the strand formed by residues 107 - 111 (chain M) in PDB entry 5A0Q
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 TYR 107 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300L KNM 5.8 3.1 - - - +
12M ILE* 4.5 3.3 - - - +
53M GLY 4.2 0.2 - - - +
54M CYS* 3.6 0.7 + - - -
55M SER* 2.4 59.6 + - - +
56M GLY* 4.2 7.4 - - - -
105M TYR* 3.8 31.4 + + - -
106M VAL* 1.4 67.4 - - - +
108M ASN* 1.3 61.4 + - - +
109M ILE* 5.1 3.7 - - + +
124M PHE 3.7 22.2 - - - +
125M ASP* 4.1 8.3 - - + -
126M PRO* 3.9 23.2 - - + +
138M GLY* 5.2 6.5 - - - -
139M GLY* 4.7 13.7 - - - +
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Residues in contact with ASN 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M ILE* 4.3 16.9 - - + +
53M GLY 3.2 8.1 - - - +
54M CYS* 2.6 31.1 - - - +
64M LEU* 3.4 17.6 - - - +
65M THR* 5.4 0.8 - - - +
92M LEU* 4.5 8.1 - - + +
96M LEU* 4.4 6.2 - - - +
106M VAL* 2.3 44.3 - - - +
107M TYR* 1.3 72.2 - - - +
109M ILE* 1.3 63.0 + - - +
110M ILE* 4.1 0.7 - - + -
122M TYR 3.3 2.4 - - - +
124M PHE* 3.0 45.4 + - + +
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Residues in contact with ILE 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ILE* 3.5 35.0 - - + -
14M ALA* 3.4 30.5 - - + -
23M VAL* 4.8 4.2 - - + +
51M VAL 4.1 0.2 - - - +
52M ILE* 3.3 4.5 - - - +
53M GLY 2.9 32.0 + - - +
107M TYR* 5.1 2.7 - - + +
108M ASN* 1.3 75.8 - - - +
110M ILE* 1.4 65.5 + - - +
121M VAL* 3.8 13.0 - - + -
122M TYR 3.5 2.0 - - - +
123M SER* 4.0 15.7 - - - +
124M PHE 4.9 1.1 - - - +
136M LYS* 3.9 37.2 - - + +
138M GLY* 4.8 8.7 - - - +
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Residues in contact with ILE 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M VAL* 5.0 1.5 - - - +
50M THR* 5.1 4.9 - - + -
51M VAL 3.9 2.5 - - - +
52M ILE* 3.5 35.9 - - + -
68M ILE* 6.0 0.4 - - + -
85M THR* 3.7 27.6 - - + +
88M ILE* 3.8 38.6 - - + -
92M LEU* 4.1 6.7 - - + -
108M ASN* 5.3 0.7 - - + -
109M ILE* 1.4 75.2 - - - +
111M GLY* 1.3 62.4 - - - +
112M GLY 4.1 2.5 - - - +
120M ALA 3.4 1.0 - - - +
121M VAL* 3.3 11.1 - - - +
122M TYR* 3.3 31.9 + - + -
124M PHE* 3.8 25.8 - - + -
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Residues in contact with GLY 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ALA* 4.4 8.7 - - - -
23M VAL* 4.5 10.4 - - - +
49M LYS 2.5 24.3 - - - +
50M THR* 4.2 0.2 - - - -
51M VAL* 2.8 26.7 + - - +
110M ILE* 1.3 75.2 - - - +
112M GLY* 1.3 52.6 + - - -
120M ALA 3.7 12.8 - - - -
198M VAL* 3.6 11.0 - - - +
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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